diff --git a/Readme.Rmd b/Readme.Rmd index 066a948..e01b35f 100644 --- a/Readme.Rmd +++ b/Readme.Rmd @@ -63,9 +63,9 @@ myresults$smurf_indel$stats_indel #Mutect2 383 #FreeBayes 85 #VarDict 166 -#VarScan 158 -#Atleast1 765 -#Atleast2 25 +#VarScan 208 +#Atleast1 810 +#Atleast2 30 #Atleast3 2 #All4 0 #SMuRF_INDEL 1 @@ -73,36 +73,30 @@ myresults$smurf_indel$stats_indel myresults$smurf_indel$predicted_indel #Chr START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs SMuRF_score -#1 "1" "17820432" "17820433" "AT/AT/AT/AT" "A/A/A/A" "0.571875" +#1 "1" "17820432" "17820433" "AT/AT/AT/AT" "A/A/A/A" "0.6210418" myresults$smurf_snv$stats_snv -# Passed_Calls -#Mutect2 5004 -#FreeBayes 115 -#VarDict 124 -#VarScan 501 -#Atleast1 5684 -#Atleast2 42 -#Atleast3 16 -#All4 2 -#SMuRF_SNV 12 - -myresults$smurf_snv$predicted_snv - -#Chr START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs TRUTH_confidence -#1 "1" "12207135" "12207135" "G/G/G/G" "A/A/A/A" "0.9941938" -#2 "1" "14955425" "14955425" "C/C/C/C" "A/A/A/A" "0.9025974" -#3 "1" "18525077" "18525077" "G/G/G/G" "A/A/A/A" "0.9972492" -#4 "1" "21459584" "21459584" "T/T/T/T" "A/A/A/A" "0.9919866" -#5 "1" " 2180985" " 2180985" "A/A/A/A" "G/G/G/G" "0.9992510" -#6 "1" "22385823" "22385823" "A/A/A/A" "G/G/G/G" "0.6207352" -#7 "1" "25322776" "25322776" "C/C/NA/C" "T/T/NA/T" "0.8995001" -#8 "1" "28317030" "28317030" "G/NA/G/G" "T/NA/T/T" "0.8962453" -#9 "1" " 5035185" " 5035185" "C/C/C/C" "T/T/T/T" "0.9321060" -#10 "1" " 8881322" " 8881322" "G/G/G/G" "A/A/A/A" "0.9116895" -#11 "1" " 8929624" " 8929624" "A/A/A/A" "G/G/G/G" "0.8765643" -#12 "1" " 9478609" " 9478609" "A/A/A/A" "G/G/G/G" "0.5984848" +# Passed_Calls +#Mutect2 5004 +#FreeBayes 115 +#VarDict 124 +#VarScan 535 +#Atleast1 5700 +#Atleast2 49 +#Atleast3 19 +#All4 10 +#SMuRF_SNV 399 + +head(myresults$smurf_snv$predicted_snv) + +#Chr START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs SMuRF_score +#1 "1" "100080141" "100080141" "T/NA/NA/NA" "A/NA/NA/NA" "0.5449806" +#2 "1" "100418794" "100418794" "G/NA/NA/NA" "T/NA/NA/NA" "0.4698960" +#3 "1" "100444255" "100444255" "A/NA/NA/NA" "T/NA/NA/NA" "0.4725965" +#4 "1" "100470006" "100470006" "C/NA/NA/NA" "A/NA/NA/NA" "0.4074448" +#5 "1" "100494646" "100494646" "G/NA/NA/NA" "T/NA/NA/NA" "0.3901333" +#6 "1" "100997475" "100997475" "C/NA/NA/NA" "A/NA/NA/NA" "0.4804897" ``` diff --git a/smurf/NAMESPACE b/smurf/NAMESPACE index c42da3b..5e42a5a 100644 --- a/smurf/NAMESPACE +++ b/smurf/NAMESPACE @@ -1,6 +1,12 @@ # Generated by roxygen2: do not edit by hand export(indelRFparse) +export(indelRFparseall) +export(indelRFparsefeatures) export(parsevcf) +export(parsevcfall) +export(parsevcffeatures) export(smurf) export(snvRFparse) +export(snvRFparseall) +export(snvRFparsefeatures) diff --git a/smurf/R/indelRFparse.R b/smurf/R/indelRFparse.R index 0199025..c7d163e 100644 --- a/smurf/R/indelRFparse.R +++ b/smurf/R/indelRFparse.R @@ -42,9 +42,9 @@ indelRFparse = function(a){ colnames(varscan)<-c("X.CHROM", "POS", "END_POS_Varscan", "REF_Varscan", "ALT_Varscan", "vs_SSC","vs_SPV") vardict<-as.data.frame(a[[7]][!isSNV(a[[7]], singleAltOnly=FALSE)],row.names=NULL) - vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF","MSI")] + vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF","MSI","SOR")] vardict<-vardict[grep("GL*", vardict$seqnames, invert=TRUE),] - colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI") + colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI","vd_SOR") #Filtering Indels from collapsed vcf mutect_Indel<-a[[2]][!isSNV(a[[2]], singleAltOnly=FALSE)] @@ -67,7 +67,9 @@ indelRFparse = function(a){ colnames(freebayes_coordinates)[1:2]<-c("X.CHROM", "POS") freebayes_coordinates<-freebayes_coordinates[grep("GL*", freebayes_coordinates$X.CHROM, invert = TRUE),] - varscan_clean_Indel<-rowRanges(varscan_Indel[varscan_Indel@fixed$FILTER=="PASS",])[,1] + #we are including the SpvFreq as PASSED calls + varscan_clean_Indel<-rowRanges(varscan_Indel[varscan_Indel@fixed$FILTER=="PASS" | varscan_Indel@fixed$FILTER=="SpvFreq",])[,1] + #varscan_clean_Indel<-rowRanges(varscan_Indel[varscan_Indel@fixed$FILTER=="PASS",])[,1] varscan_coordinates<-as.data.frame(unlist(varscan_clean_Indel),row.names=NULL) varscan_coordinates<-varscan_coordinates[1:2] varscan_coordinates$FILTER_Varscan<-"PASS" @@ -88,9 +90,15 @@ indelRFparse = function(a){ coordinates<-unique(coordinates) #Pulling out calls from VRanges object for each caller using coordinates + m2<-dim(mutect)[2] mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) mutect<-unique(mutect) - mutect<-mutect[,1:(dim(mutect)[2]-3)] + M_2<-which( colnames(mutect)=="FILTER_Mutect2" ) + mutect<-mutect[,c(1:m2,M_2)] + + # mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) + # mutect<-unique(mutect) + # mutect<-mutect[,1:(dim(mutect)[2]-3)] fb<-dim(freebayes)[2] freebayes<-merge(freebayes, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) @@ -128,16 +136,16 @@ indelRFparse = function(a){ final<-final[,c("X.CHROM", "POS", "END_POS", "REF", "ALT", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", "m2_MQ","m2_MQRankSum","m2_NLOD","m2_TLOD", "f_LEN", - "vs_SSC","vs_SPV","vd_SSF","vd_MSI")] + "vs_SSC","vs_SPV","vd_SSF","vd_MSI","vd_SOR")] colnames(final)<-c("X.CHROM", "START_POS_REF", "END_POS_REF", "REF_MFVdVs", "ALT_MFVdVs", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", "m2_MQ","m2_MQRankSum","m2_NLOD","m2_TLOD", "f_LEN", - "vs_SSC","vs_SPV","vd_SSF","vd_MSI") + "vs_SSC","vs_SPV","vd_SSF","vd_MSI","vd_SOR") #Removing Duplicates for(i in c("m2_MQ","m2_MQRankSum","m2_NLOD","m2_TLOD", "f_LEN", - "vs_SSC","vs_SPV","vd_SSF","vd_MSI")) + "vs_SSC","vs_SPV","vd_SSF","vd_MSI", "vd_SOR")) { final[,i]<-as.numeric(final[,i]) } @@ -153,14 +161,18 @@ indelRFparse = function(a){ final[,i] <- as.logical(final[,i]) } + final$vd_SOR[which(is.infinite(final$vd_SOR)==TRUE)] <- 0 + indel_parse <- final print("Predicting INDELs") df <- final[,c("X.CHROM","START_POS_REF","FILTER_Mutect2","FILTER_Freebayes","FILTER_Vardict","FILTER_Varscan", - "m2_MQ","m2_MQRankSum","m2_NLOD","m2_TLOD","f_LEN","vs_SSC","vs_SPV","vd_SSF","vd_MSI")] - write.csv(df, 'indel_parse.csv',row.names = F) - df <- h2o.importFile(path = normalizePath("indel_parse.csv"),header=T) + "m2_MQ","m2_MQRankSum","m2_NLOD","m2_TLOD","f_LEN","vs_SSC","vs_SPV","vd_SSF","vd_MSI","vd_SOR")] + df <- as.h2o(df) + + # write.csv(df, 'indel_parse.csv',row.names = F) + # df <- h2o.importFile(path = normalizePath("indel_parse.csv"),header=T) smurfdir <- find.package("smurf") smurfmodeldir <- paste0(smurfdir, "/data/indel-model-combined-grid") @@ -168,11 +180,10 @@ indelRFparse = function(a){ #indel_model <- h2o.loadModel(path = "/home/huangwt/R/x86_64-pc-linux-gnu-library/3.3/smbio/data/indel_model-combined-0205") #indel_model <- h2o.loadModel(path = "D:/Users/Tyler/Dropbox/Scripts/Real-v3/Results-Indels-v3/indel_model-combined-0205") - #indel_model <- h2o.loadModel(path = "C:/Users/Tyler/Dropbox/Scripts/smurf/smurf1.0/data/indel-model-combined-grid") + #indel_model <- h2o.loadModel(path = "D:/Users/Tyler/Dropbox/SMuRFv1.1/smurf/data/indel-model-combined-grid") predicted <- h2o.predict(object = indel_model, newdata = df) - - suppressMessages(file.remove("indel_parse.csv")) + #suppressMessages(file.remove("indel_parse.csv")) p <- as.data.frame(predicted) table <- final @@ -198,7 +209,7 @@ indelRFparse = function(a){ colnames(stats) <- c("Passed_Calls") rownames(stats) <- c("Mutect2", "FreeBayes", "VarDict", "VarScan", "Atleast1", "Atleast2", "Atleast3", "All4", "SMuRF_INDEL") - counts <- apply(table[, c(6,7,8,9)], 1, function(x) length(which(x=="TRUE"))) + counts <- apply(table[, c("FILTER_Mutect2","FILTER_Freebayes","FILTER_Vardict","FILTER_Varscan")], 1, function(x) length(which(x=="TRUE"))) stats$Passed_Calls[1] <- length(which((table$FILTER_Mutect2==TRUE))) stats$Passed_Calls[2] <- length(which((table$FILTER_Freebayes==TRUE))) diff --git a/smurf/R/indelRFparseall.R b/smurf/R/indelRFparseall.R deleted file mode 100644 index 6309497..0000000 --- a/smurf/R/indelRFparseall.R +++ /dev/null @@ -1,224 +0,0 @@ -#' indelRF-Parse -#' -#' Indel prediction model -#' Step 1 Parse -#' -#' -#' @examples -#' -#' -#' @export -indelRFparseall = function(a){ - - print("indelRF Parsing") - - #Filtering Indels from VRanges object - mutect<-as.data.frame(a[[1]][!isSNV(a[[1]], singleAltOnly=FALSE)],row.names=NULL) - #mutect<-mutect[mutect$sampleNames == samples(header(a[[2]]))[1],] - mutect<-mutect[,c("seqnames","start","end", "ref", "alt", "BaseQRankSum","ClippingRankSum","FS","HCNT","MQ","MQRankSum","NLOD","ReadPosRankSum","TLOD")] - mutect<-mutect[grep("GL*", mutect$seqnames, invert=TRUE),] - colnames(mutect)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD") - - freebayes<-as.data.frame(a[[3]][!isSNV(a[[3]], singleAltOnly=FALSE)],row.names=NULL) - freebayes<-freebayes[,c("seqnames","start","end", "ref", "alt", "AB","ABP","EPP","EPPR","GTI","LEN","MQM","MQMR","NS","NUMALT","ODDS","PAIRED","PAIREDR","RPP","SAP","SRP")] - freebayes<-freebayes[grep("GL*", freebayes$seqnames, invert=TRUE),] - #freebayes_GQT<-freebayes[freebayes$sampleNames == samples(header(a[[2]]))[1],] #[1] for tumor - #freebayes_GQT<-freebayes_GQT[,c("seqnames","start","end", "ref", "alt","QUAL","GQ")] - #colnames(freebayes_GQT)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","QUAL","GQ-T") - #freebayes_GQN<-freebayes[freebayes$sampleNames == samples(header(a[[2]]))[2],] - #freebayes_GQN<-freebayes_GQN[,c("sampleNames","GQ")] - #colnames(freebayes_GQN)<-c("sampleNames","GQ-N") - #freebayes<-cbind(freebayes_GQT, freebayes_GQN) - #freebayes_GQN<-freebayes[freebayes$sampleNames == samples(header(a[[2]]))[2],] #[2] for normal - #freebayes_GQN<-freebayes_GQN[,c("seqnames","start","end", "ref", "alt","QUAL","GQ")] - #colnames(freebayes_GQN)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","GQ-N") - #freebayes <- freebayes_GQN - #freebayes<-freebayes[,c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes")] - colnames(freebayes)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP") - - varscan<-as.data.frame(a[[5]][!isSNV(a[[5]], singleAltOnly=FALSE)],row.names=NULL) - varscan<-varscan[,c("seqnames","start","end", "ref", "alt", "SSC","GPV","SS","SPV")] - varscan<-varscan[grep("GL*", varscan$seqnames, invert=TRUE),] - colnames(varscan)<-c("X.CHROM", "POS", "END_POS_Varscan", "REF_Varscan", "ALT_Varscan", "vs_SSC","vs_GPV","vs_SS","vs_SPV") - - vardict<-as.data.frame(a[[7]][!isSNV(a[[7]], singleAltOnly=FALSE)],row.names=NULL) - vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF","MSI","SOR")] - vardict<-vardict[grep("GL*", vardict$seqnames, invert=TRUE),] - colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI","vd_SOR") - - - #### Coding annotation #### - - #Filtering Indels from VRanges object - mutect_cds<-as.data.frame(a[[9]][!isSNV(a[[9]], singleAltOnly=FALSE)],row.names=NULL) - mutect_cds<-mutect_cds[,c("seqnames","start","end", "ref", "alt", "BaseQRankSum","ClippingRankSum","FS","HCNT","MQ","MQRankSum","NLOD","ReadPosRankSum","TLOD")] - mutect_cds<-mutect_cds[grep("GL*", mutect_cds$seqnames, invert=TRUE),] - colnames(mutect_cds)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD") - - freebayes_cds<-as.data.frame(a[[11]][!isSNV(a[[11]], singleAltOnly=FALSE)],row.names=NULL) - freebayes_cds<-freebayes_cds[,c("seqnames","start","end", "ref", "alt", "AB","ABP","EPP","EPPR","GTI","LEN","MQM","MQMR","NS","NUMALT","ODDS","PAIRED","PAIREDR","RPP","SAP","SRP")] - freebayes_cds<-freebayes_cds[grep("GL*", freebayes_cds$seqnames, invert=TRUE),] - colnames(freebayes_cds)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP") - - varscan_cds<-as.data.frame(a[[13]][!isSNV(a[[13]], singleAltOnly=FALSE)],row.names=NULL) - varscan_cds<-varscan_cds[,c("seqnames","start","end", "ref", "alt", "SSC","GPV","SS","SPV")] - varscan_cds<-varscan_cds[grep("GL*", varscan_cds$seqnames, invert=TRUE),] - colnames(varscan_cds)<-c("X.CHROM", "POS", "END_POS_Varscan", "REF_Varscan", "ALT_Varscan", "vs_SSC","vs_GPV","vs_SS","vs_SPV") - - vardict_cds<-as.data.frame(a[[15]][!isSNV(a[[15]], singleAltOnly=FALSE)],row.names=NULL) - vardict_cds<-vardict_cds[,c("seqnames","start","end", "ref", "alt", "SSF","MSI","SOR")] - vardict_cds<-vardict_cds[grep("GL*", vardict_cds$seqnames, invert=TRUE),] - colnames(vardict_cds)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI","vd_SOR") - - #assign column and then merge with original - mutect_cds$Region <- "CDS" - mutect_cds <- mutect_cds[,c(1,2,dim(mutect_cds)[2])] - mutect_cds <- unique(mutect_cds) - mutect<-merge(mutect, mutect_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #mutect[which(is.na(mutect[,dim(mutect)[2]])), dim(mutect)[2]] <- "Non-coding" - - freebayes_cds$Region <- "CDS" - freebayes_cds <- freebayes_cds[,c(1,2,dim(freebayes_cds)[2])] - freebayes_cds <- unique(freebayes_cds) - freebayes<-merge(freebayes, freebayes_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #freebayes[which(is.na(freebayes[,dim(freebayes)[2]])), dim(freebayes)[2]] <- "Non-coding" - - varscan_cds$Region <- "CDS" - varscan_cds <- varscan_cds[,c(1,2,dim(varscan_cds)[2])] - varscan_cds <- unique(varscan_cds) - varscan<-merge(varscan, varscan_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #varscan[which(is.na(varscan[,dim(varscan)[2]])), dim(varscan)[2]] <- "Non-coding" - - vardict_cds$Region <- "CDS" - vardict_cds <- vardict_cds[,c(1,2,dim(vardict_cds)[2])] - vardict_cds <- unique(vardict_cds) - vardict<-merge(vardict, vardict_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #vardict[which(is.na(vardict[,dim(vardict)[2]])), dim(vardict)[2]] <- "Non-coding" - - - #### Coordinates filtering #### - - - #Filtering Indels from collapsed vcf - mutect_Indel<-a[[2]][!isSNV(a[[2]], singleAltOnly=FALSE)] - freebayes_Indel<-a[[4]][!isSNV(a[[4]], singleAltOnly=FALSE)] - varscan_Indel<-a[[6]][!isSNV(a[[6]], singleAltOnly=FALSE)] - vardict_Indel<-a[[8]][!isSNV(a[[8]], singleAltOnly=FALSE)] - - ## Filtering Passed calls from raw file - mutect_clean_Indel<-rowRanges(mutect_Indel[mutect_Indel@fixed$FILTER=="PASS",])[,1] - mutect_coordinates<-as.data.frame(unlist(mutect_clean_Indel),row.names=NULL) - mutect_coordinates<-mutect_coordinates[1:2] - mutect_coordinates$FILTER_Mutect2<-"PASS" - colnames(mutect_coordinates)[1:2]<-c("X.CHROM", "POS") - mutect_coordinates<-mutect_coordinates[grep("GL*", mutect_coordinates$X.CHROM, invert = TRUE),] - - freebayes_clean_Indel<-rowRanges(freebayes_Indel[freebayes_Indel@fixed$FILTER=="PASS",])[,1] - freebayes_coordinates<-as.data.frame(unlist(freebayes_clean_Indel),row.names=NULL) - freebayes_coordinates<-freebayes_coordinates[1:2] - freebayes_coordinates$FILTER_Freebayes<-"PASS" - colnames(freebayes_coordinates)[1:2]<-c("X.CHROM", "POS") - freebayes_coordinates<-freebayes_coordinates[grep("GL*", freebayes_coordinates$X.CHROM, invert = TRUE),] - - #we are including the SpvFreq as PASSED calls - varscan_clean_Indel<-rowRanges(varscan_Indel[varscan_Indel@fixed$FILTER=="PASS" | varscan_Indel@fixed$FILTER=="SpvFreq",])[,1] - varscan_coordinates<-as.data.frame(unlist(varscan_clean_Indel),row.names=NULL) - varscan_coordinates<-varscan_coordinates[1:2] - varscan_coordinates$FILTER_Varscan<-"PASS" - colnames(varscan_coordinates)[1:2]<-c("X.CHROM", "POS") - varscan_coordinates<-varscan_coordinates[grep("GL*", varscan_coordinates$X.CHROM, invert = TRUE),] - - vardict_clean_Indel<-rowRanges(vardict_Indel[vardict_Indel@fixed$FILTER=="PASS",])[,1] - vardict_coordinates<-as.data.frame(unlist(vardict_clean_Indel),row.names=NULL) - vardict_coordinates<-vardict_coordinates[1:2] - vardict_coordinates$FILTER_Vardict<-"PASS" - colnames(vardict_coordinates)[1:2]<-c("X.CHROM", "POS") - vardict_coordinates<-vardict_coordinates[grep("GL*", vardict_coordinates$X.CHROM, invert = TRUE),] - - #All Pass coordinates(i.e., coordinates passed by at least one caller) - f1<-merge(mutect_coordinates, freebayes_coordinates, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - f2<-merge(varscan_coordinates, vardict_coordinates, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - coordinates<-merge(f1, f2, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - coordinates<-unique(coordinates) - - #Pulling out calls from VRanges object for each caller using coordinates - m2<-dim(mutect)[2] - mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - mutect<-unique(mutect) - M_2<-which( colnames(mutect)=="FILTER_Mutect2" ) - mutect<-mutect[,c(1:m2,M_2)] - - fb<-dim(freebayes)[2] - freebayes<-merge(freebayes, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - freebayes<-unique(freebayes) - F_B<-which( colnames(freebayes)=="FILTER_Freebayes" ) - freebayes<-freebayes[,c(1:fb,F_B)] - - vs<-dim(varscan)[2] - varscan<-merge(varscan, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - varscan<-unique(varscan) - V_S<-which( colnames(varscan)=="FILTER_Varscan" ) - varscan<-varscan[,c(1:vs,V_S)] - - vd<-dim(vardict)[2] - vardict<-merge(vardict, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - vardict<-unique(vardict) - V_D<-which( colnames(vardict)=="FILTER_Vardict" ) - vardict<-vardict[,c(1:vd,V_D)] - - #Merging all calls from each caller - f1<-merge(mutect, freebayes, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - f2<-merge(varscan, vardict, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - - final<-merge(f1,f2, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - final[which(is.na(final[,c("Region")])), c("Region")] <- "Non-coding" - - raw <- final - - - - #Formatting - final$REF<-paste(final$REF_Mutect2,final$REF_Freebayes,final$REF_Vardict,final$REF_Varscan, sep ="/") - final$ALT<-paste(final$ALT_Mutect2,final$ALT_Freebayes,final$ALT_Vardict,final$ALT_Varscan, sep ="/") - f<-subset(final,select=c("END_POS_Mutect2", "END_POS_Freebayes", "END_POS_Vardict", "END_POS_Varscan")) - final$END_POS<-apply(f, MARGIN=1, function(x) max(x,na.rm=TRUE)) - final<-final[,c("X.CHROM", "POS", "END_POS", "REF", "ALT", "Region", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD", - "f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP", - "vs_SSC","vs_GPV","vs_SS","vs_SPV","vd_SSF","vd_MSI","vd_SOR")] - colnames(final)<-c("X.CHROM", "START_POS_REF", "END_POS_REF", "REF_MFVdVs", "ALT_MFVdVs", "REGION", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD", - "f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP", - "vs_SSC","vs_GPV","vs_SS","vs_SPV","vd_SSF","vd_MSI","vd_SOR") - - - for(i in 11:dim(final)[2]) - { - final[,i]<-as.numeric(final[,i]) - } - - #Removing Duplicates - final<-unique(final) - - for(i in c("FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan")) - { - final[which(is.na(final[,i])), i] <- FALSE - final[which(final[,i]!="PASS"), i] <- "FALSE" - final[which(final[,i]=="PASS"), i] <- "TRUE" - final[,i] <- as.logical(final[,i]) - } - - final$vd_SOR[which(is.infinite(final$vd_SOR)==TRUE)] <- 0 - - - final<-as.matrix(final) - z <- list(final) - names(z)<- c("allfeatures_indel") - return(z) - - #write.table(final , file = "indel-parse-allfeatures.txt", sep = "\t", quote = FALSE, row.names = FALSE) - #x = read.table('indel-parse-allfeatures.txt',header=T,sep = "\t") - #write.csv(x, 'indel-parse-allfeatures.csv',row.names = F) - - -} diff --git a/smurf/R/parsevcf.R b/smurf/R/parsevcf.R index 9ceb8c6..8eb8624 100644 --- a/smurf/R/parsevcf.R +++ b/smurf/R/parsevcf.R @@ -1,4 +1,4 @@ -#' parse +#' parsevcf #' #' Initial file parse and preparation before filtering #' @@ -14,7 +14,7 @@ parsevcf = function(x){ #ScanVCF with required parameters svp_m<-ScanVcfParam(info=c("MQ","MQRankSum","TLOD","NLOD"),geno=NA) - svp_f<-ScanVcfParam(info=c("MQM","MQMR","ODDS","LEN"),geno=NA) + svp_f<-ScanVcfParam(info=c("MQM","MQMR","LEN"),geno=NA) svp_vs<-ScanVcfParam(info=c("SSC","SPV"), geno=NA) svp_vd<-ScanVcfParam(info=c("SSF","SOR","MSI"), geno=NA) @@ -28,7 +28,9 @@ parsevcf = function(x){ obj7<- suppressWarnings(readVcf(x[[4]], "hg19", svp_vd)) obj8<-suppressWarnings(as(obj7, "VRanges")) - a<-list("mutect_raw"=obj2, "mutect_vcf"=obj1, "freebayes_raw"=obj4, "freebayes_vcf"=obj3, "varscan_raw"=obj6, "varscan_vcf"=obj5, "vardict_raw"=obj8, "vardict_vcf"=obj7) + a<-list("mutect_raw"=obj2, "mutect_vcf"=obj1, "freebayes_raw"=obj4, "freebayes_vcf"=obj3, + "varscan_raw"=obj6, "varscan_vcf"=obj5, "vardict_raw"=obj8, "vardict_vcf"=obj7) return(a) } + diff --git a/smurf/R/parsevcfall.R b/smurf/R/parsevcfall.R deleted file mode 100644 index f155dc0..0000000 --- a/smurf/R/parsevcfall.R +++ /dev/null @@ -1,57 +0,0 @@ -#' parse -#' -#' Initial file parse and preparation before filtering -#' -#' @param filedir Sets the working directory containing the vcf.gz files from -#' callers MuTect2, Freebayes, VarDict and VarScan. -#' -#' -#' @examples -#' -#' -#' @export -parsevcfall = function(x){ - - - #ScanVCF with required parameters - svp_m<-ScanVcfParam(info=c("BaseQRankSum","ClippingRankSum","FS","HCNT","MQ","MQRankSum","NLOD","ReadPosRankSum","TLOD"),geno=NA) - svp_f<-ScanVcfParam(info=c("AB","ABP","EPP","EPPR","GTI","LEN","MQM","MQMR","NS","NUMALT","ODDS","PAIRED","PAIREDR","RPP","SAP","SRP"),geno=NA) - svp_vs<-ScanVcfParam(info=c("SSC","GPV","SS","SPV"), geno=NA) - svp_vd<-ScanVcfParam(info=c("SSF","MSI","SOR"), geno=NA) - - #Read Vcf of each caller and Convert collapsed vcf to VRanges object - obj1<- readVcf(x[[1]], "hg19", svp_m) - obj2<-as(obj1, "VRanges") - obj3<- readVcf(x[[2]], "hg19",svp_f) - obj4<-as(obj3, "VRanges") - obj5<- readVcf(x[[3]], "hg19", svp_vs) - obj6<-as(obj5, "VRanges") - obj7<- readVcf(x[[4]], "hg19", svp_vd) - obj8<-as(obj7, "VRanges") - - - - obj1cds<- readVcf(x[[5]], "hg19", svp_m) - obj2cds<-as(obj1cds, "VRanges") - obj3cds<- readVcf(x[[6]], "hg19",svp_f) - obj4cds<-as(obj3cds, "VRanges") - obj5cds<- readVcf(x[[7]], "hg19", svp_vs) - obj6cds<-as(obj5cds, "VRanges") - obj7cds<- readVcf(x[[8]], "hg19", svp_vd) - obj8cds<-as(obj7cds, "VRanges") - - # a<-list("mutect_raw"=obj2, "mutect_vcf"=obj1, "freebayes_raw"=obj4, "freebayes_vcf"=obj3, - # "varscan_raw"=obj6, "varscan_vcf"=obj5, "vardict_raw"=obj8, "vardict_vcf"=obj7 - # ) - - a<-list("mutect_raw"=obj2, "mutect_vcf"=obj1, "freebayes_raw"=obj4, "freebayes_vcf"=obj3, - "varscan_raw"=obj6, "varscan_vcf"=obj5, "vardict_raw"=obj8, "vardict_vcf"=obj7, - "mutect_raw_cds"=obj2cds, "mutect_vcf_cds"=obj1cds, "freebayes_raw_cds"=obj4cds, "freebayes_vcf_cds"=obj3cds, - "varscan_raw_cds"=obj6cds, "varscan_vcf_cds"=obj5cds, "vardict_raw_cds"=obj8cds, "vardict_vcf_cds"=obj7cds - ) - - return(a) - - -} - diff --git a/smurf/R/smurf.R b/smurf/R/smurf.R index e52adb1..53c2d95 100644 --- a/smurf/R/smurf.R +++ b/smurf/R/smurf.R @@ -1,4 +1,4 @@ -#' SMuRF +#' SMuRF v1.1 #' #' Somatic mutation consensus calling based on four callers: #' MuTect2, Freebayes, VarDict, VarScan @@ -159,16 +159,28 @@ smurf = function(directory, model){ return(list("smurf_snv"=y,"smurf_indel"=z,"time.taken"=time.taken)) } - # - # if (model == "features") { #new model with REGION column - # start.time <- Sys.time() - # a<-parsevcffeatures(x) - # y<-snvRFparsefeatures(a) - # z<-indelRFparsefeatures(a) - # smbio_sm<<-list("smbio_snv"=y,"smbio_indel"=z) - # end.time <- Sys.time() - # time.taken <<- end.time - start.time - # } + + if (model == "features") { #new model with REGION column + print("Initializing CDS and feature extraction.") + start.time <- Sys.time() + + #to include CDS calls + m2 <- paste(directory,list.files(directory,pattern="CDS_mutect2.vcf", full.names=F), sep = "") + fb <- paste(directory,list.files(directory,pattern="CDS_freebayes.vcf", full.names=F), sep = "") + vs <- paste(directory,list.files(directory,pattern="CDS_varscan.vcf", full.names=F), sep = "") + vd <- paste(directory,list.files(directory,pattern="CDS_vardict.vcf", full.names=F), sep = "") + + x<-list(mutect2,freebayes,varscan,vardict,m2,fb,vs,vd) + + a<-parsevcffeatures(x) + y<-snvRFparsefeatures(a) + z<-indelRFparsefeatures(a) + end.time <- Sys.time() + time.taken <<- end.time - start.time + #smbio_sm<<-list("smbio_snv"=y,"smbio_indel"=z) + return(list("smurf_snv"=y,"smurf_indel"=z,"time.taken"=time.taken)) + + } } else { print("Error: Input file check failed. One or more files may be missing or duplicated.") diff --git a/smurf/R/snvRFparse.R b/smurf/R/snvRFparse.R index 18eabae..147d8f2 100644 --- a/smurf/R/snvRFparse.R +++ b/smurf/R/snvRFparse.R @@ -16,14 +16,14 @@ snvRFparse = function(a){ #Filtering SNVs from VRanges object along with features mutect<-as.data.frame(a[[1]][isSNV(a[[1]], singleAltOnly=FALSE)],row.names=NULL) #mutect<-mutect[mutect$sampleNames == samples(header(a[[2]]))[1],] - mutect<-mutect[,c("seqnames","start","end", "ref", "alt", "MQ","MQRankSum","TLOD")] + mutect<-mutect[,c("seqnames","start","end", "ref", "alt", "MQ","MQRankSum","TLOD","NLOD")] mutect<-mutect[grep("GL*", mutect$seqnames, invert=TRUE),] - colnames(mutect)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_MQ","m2_MQRankSum","m2_TLOD") + colnames(mutect)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_MQ","m2_MQRankSum","m2_TLOD","m2_NLOD") freebayes<-as.data.frame(a[[3]][isSNV(a[[3]], singleAltOnly=FALSE)],row.names=NULL) - freebayes<-freebayes[,c("seqnames","start","end", "ref", "alt","MQM","MQMR","ODDS")] + freebayes<-freebayes[,c("seqnames","start","end", "ref", "alt","MQM","MQMR")] freebayes<-freebayes[grep("GL*", freebayes$seqnames, invert=TRUE),] - colnames(freebayes)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_MQM","f_MQMR","f_ODDS") + colnames(freebayes)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_MQM","f_MQMR") varscan<-as.data.frame(a[[5]][isSNV(a[[5]], singleAltOnly=FALSE)],row.names=NULL) varscan<-varscan[,c("seqnames","start","end", "ref", "alt", "SSC","SPV")] @@ -32,9 +32,9 @@ snvRFparse = function(a){ vardict<-as.data.frame(a[[7]][isSNV(a[[7]], singleAltOnly=FALSE)],row.names=NULL) #vardict<-vardict[vardict$sampleNames == samples(header(a[[2]]))[1],] #choose only the tumor sample values (1 or 2) eg.icgc_cll-T - vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF","SOR")] + vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF")] vardict<-vardict[grep("GL*", vardict$seqnames, invert=TRUE),] - colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_SOR") + colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF") #Filtering SNV's from collapsed vcf mutect_SNV<-a[[2]][isSNV(a[[2]], singleAltOnly=FALSE)] @@ -57,7 +57,9 @@ snvRFparse = function(a){ colnames(freebayes_coordinates)[1:2]<-c("X.CHROM", "POS") freebayes_coordinates<-freebayes_coordinates[grep("GL*", freebayes_coordinates$X.CHROM, invert = TRUE),] - varscan_clean_SNV<-rowRanges(varscan_SNV[varscan_SNV@fixed$FILTER=="PASS",])[,1] + #we are including the SpvFreq as PASSED calls + varscan_clean_SNV<-rowRanges(varscan_SNV[varscan_SNV@fixed$FILTER=="PASS" | varscan_SNV@fixed$FILTER=="SpvFreq",])[,1] + #varscan_clean_SNV<-rowRanges(varscan_SNV[varscan_SNV@fixed$FILTER=="PASS",])[,1] varscan_coordinates<-as.data.frame(unlist(varscan_clean_SNV),row.names=NULL) varscan_coordinates<-varscan_coordinates[1:2] varscan_coordinates$FILTER_Varscan<-"PASS" @@ -78,10 +80,16 @@ snvRFparse = function(a){ coordinates<-unique(coordinates) #Pulling out calls from VRanges object for each caller using coordinates + m2<-dim(mutect)[2] mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) mutect<-unique(mutect) - mutect<-mutect[,1:(dim(mutect)[2]-3)] - + M_2<-which( colnames(mutect)=="FILTER_Mutect2" ) + mutect<-mutect[,c(1:m2,M_2)] + + # mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) + # mutect<-unique(mutect) + # mutect<-mutect[,1:(dim(mutect)[2]-3)] + # fb<-dim(freebayes)[2] freebayes<-merge(freebayes, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) freebayes<-unique(freebayes) @@ -114,15 +122,15 @@ snvRFparse = function(a){ f<-subset(final,select=c("END_POS_Mutect2", "END_POS_Freebayes", "END_POS_Vardict", "END_POS_Varscan")) final$END_POS<-apply(f, MARGIN=1, function(x) max(x,na.rm=TRUE)) final<-final[,c("X.CHROM", "POS", "END_POS", "REF", "ALT", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_MQ","m2_MQRankSum","m2_TLOD", - "f_MQM","f_MQMR","f_ODDS", - "vs_SSC","vs_SPV","vd_SSF","vd_SOR")] + "m2_MQ","m2_MQRankSum","m2_TLOD","m2_NLOD", + "f_MQM","f_MQMR", + "vs_SSC","vs_SPV","vd_SSF")] colnames(final)<-c("X.CHROM", "START_POS_REF", "END_POS_REF", "REF_MFVdVs", "ALT_MFVdVs", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_MQ","m2_MQRankSum","m2_TLOD", - "f_MQM","f_MQMR","f_ODDS", - "vs_SSC","vs_SPV","vd_SSF","vd_SOR") + "m2_MQ","m2_MQRankSum","m2_TLOD","m2_NLOD", + "f_MQM","f_MQMR", + "vs_SSC","vs_SPV","vd_SSF") - for(i in c("m2_MQ","m2_MQRankSum","m2_TLOD","f_MQM","f_MQMR","f_ODDS","vs_SSC","vs_SPV","vd_SSF","vd_SOR")) + for(i in c("m2_MQ","m2_MQRankSum","m2_TLOD","m2_NLOD","f_MQM","f_MQMR","vs_SSC","vs_SPV","vd_SSF")) { final[,i]<-as.numeric(final[,i]) } @@ -139,7 +147,7 @@ snvRFparse = function(a){ final[,i] <- as.logical(final[,i]) } - final$vd_SOR[which(is.infinite(final$vd_SOR)==TRUE)] <- 0 + #final$vd_SOR[which(is.infinite(final$vd_SOR)==TRUE)] <- 0 #summary(final) #snv_parse1<-final @@ -155,9 +163,10 @@ snvRFparse = function(a){ print("Predicting SNVs") df <- final[,c("X.CHROM","START_POS_REF","FILTER_Mutect2","FILTER_Freebayes","FILTER_Vardict","FILTER_Varscan", - "m2_MQ","m2_MQRankSum","m2_TLOD","f_MQM","f_MQMR","f_ODDS","vs_SSC","vs_SPV","vd_SSF","vd_SOR")] - write.csv(df, 'snv_parse.csv',row.names = F) - df <- h2o.importFile(path = normalizePath("snv_parse.csv"),header=T) + "m2_MQ","m2_MQRankSum","m2_TLOD","m2_NLOD","f_MQM","f_MQMR","vs_SSC","vs_SPV","vd_SSF")] + df <- as.h2o(df) + # write.csv(df, 'snv_parse.csv',row.names = F) + # df <- h2o.importFile(path = normalizePath("snv_parse.csv"),header=T) smurfdir <- find.package("smurf") smurfmodeldir <- paste0(smurfdir, "/data/snv-model-combined-grid") @@ -165,10 +174,10 @@ snvRFparse = function(a){ #snv_model <- h2o.loadModel(path = "/home/huangwt/R/x86_64-pc-linux-gnu-library/3.3/smbio/data/snv_model-combined-0221") #snv_model <- h2o.loadModel(path = "D:/Users/Tyler/Dropbox/Scripts/Real-v3/Results-snv-v3/snv_model-combined-0310") - #snv_model <- h2o.loadModel(path = "C:/Users/Tyler/Dropbox/SMuRF/smurf/data/snv-model-combined-grid") + #snv_model <- h2o.loadModel(path = "D:/Users/Tyler/Dropbox/SMuRFv1.1/smurf/data/snv-model-combined-grid") predicted <- h2o.predict(object = snv_model, newdata = df) - suppressMessages(file.remove("snv_parse.csv")) + #suppressMessages(file.remove("snv_parse.csv")) p <- as.data.frame(predicted) table <- final diff --git a/smurf/R/snvRFparseall.R b/smurf/R/snvRFparseall.R deleted file mode 100644 index b4820ae..0000000 --- a/smurf/R/snvRFparseall.R +++ /dev/null @@ -1,218 +0,0 @@ -#' snvRF-Parse -#' -#' snv prediction model -#' Step 1 Parse -#' -#' -#' @examples -#' -#' -#' @export -snvRFparseall = function(a){ - - #a<-x - print("snvRF Parsing") - - #Filtering SNVs from VRanges object along with features - mutect<-as.data.frame(a[[1]][isSNV(a[[1]], singleAltOnly=FALSE)],row.names=NULL) - #mutect<-mutect[mutect$sampleNames == samples(header(a[[2]]))[1],] - mutect<-mutect[,c("seqnames","start","end", "ref", "alt", "BaseQRankSum","ClippingRankSum","FS","HCNT","MQ","MQRankSum","NLOD","ReadPosRankSum","TLOD")] - mutect<-mutect[grep("GL*", mutect$seqnames, invert=TRUE),] - colnames(mutect)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD") - - freebayes<-as.data.frame(a[[3]][isSNV(a[[3]], singleAltOnly=FALSE)],row.names=NULL) - freebayes<-freebayes[,c("seqnames","start","end", "ref", "alt","AB","ABP","EPP","EPPR","GTI","LEN","MQM","MQMR","NS","NUMALT","ODDS","PAIRED","PAIREDR","RPP","SAP","SRP")] - freebayes<-freebayes[grep("GL*", freebayes$seqnames, invert=TRUE),] - colnames(freebayes)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP") - - varscan<-as.data.frame(a[[5]][isSNV(a[[5]], singleAltOnly=FALSE)],row.names=NULL) - varscan<-varscan[,c("seqnames","start","end", "ref", "alt", "SSC","GPV","SS","SPV")] - varscan<-varscan[grep("GL*", varscan$seqnames, invert=TRUE),] - colnames(varscan)<-c("X.CHROM", "POS", "END_POS_Varscan", "REF_Varscan", "ALT_Varscan", "vs_SSC","vs_GPV","vs_SS","vs_SPV") - - vardict<-as.data.frame(a[[7]][isSNV(a[[7]], singleAltOnly=FALSE)],row.names=NULL) - #vardict<-vardict[vardict$sampleNames == samples(header(a[[2]]))[1],] #choose only the tumor sample values (1 or 2) eg.icgc_cll-T - vardict<-vardict[,c("seqnames","start","end", "ref", "alt", "SSF","MSI","SOR")] - vardict<-vardict[grep("GL*", vardict$seqnames, invert=TRUE),] - colnames(vardict)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI","vd_SOR") - - #### Coding annotation #### - - #Filtering SNVs from VRanges object along with features - mutect_cds<-as.data.frame(a[[9]][isSNV(a[[9]], singleAltOnly=FALSE)],row.names=NULL) - #mutect_cds<-mutect_cds[mutect_cds$sampleNames == samples(header(a[[2]]))[1],] - mutect_cds<-mutect_cds[,c("seqnames","start","end", "ref", "alt", "BaseQRankSum","ClippingRankSum","FS","HCNT","MQ","MQRankSum","NLOD","ReadPosRankSum","TLOD")] - mutect_cds<-mutect_cds[grep("GL*", mutect_cds$seqnames, invert=TRUE),] - colnames(mutect_cds)<-c("X.CHROM", "POS", "END_POS_Mutect2", "REF_Mutect2", "ALT_Mutect2", "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD") - - freebayes_cds<-as.data.frame(a[[11]][isSNV(a[[11]], singleAltOnly=FALSE)],row.names=NULL) - freebayes_cds<-freebayes_cds[,c("seqnames","start","end", "ref", "alt","AB","ABP","EPP","EPPR","GTI","LEN","MQM","MQMR","NS","NUMALT","ODDS","PAIRED","PAIREDR","RPP","SAP","SRP")] - freebayes_cds<-freebayes_cds[grep("GL*", freebayes_cds$seqnames, invert=TRUE),] - colnames(freebayes_cds)<-c("X.CHROM", "POS", "END_POS_Freebayes", "REF_Freebayes", "ALT_Freebayes","f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP") - - varscan_cds<-as.data.frame(a[[13]][isSNV(a[[13]], singleAltOnly=FALSE)],row.names=NULL) - varscan_cds<-varscan_cds[,c("seqnames","start","end", "ref", "alt", "SSC","GPV","SS","SPV")] - varscan_cds<-varscan_cds[grep("GL*", varscan_cds$seqnames, invert=TRUE),] - colnames(varscan_cds)<-c("X.CHROM", "POS", "END_POS_Varscan", "REF_Varscan", "ALT_Varscan", "vs_SSC","vs_GPV","vs_SS","vs_SPV") - - vardict_cds<-as.data.frame(a[[15]][isSNV(a[[15]], singleAltOnly=FALSE)],row.names=NULL) - #vardict_cds<-vardict_cds[vardict_cds$sampleNames == samples(header(a[[2]]))[1],] #choose only the tumor sample values (1 or 2) eg.icgc_cll-T - vardict_cds<-vardict_cds[,c("seqnames","start","end", "ref", "alt", "SSF","MSI","SOR")] - vardict_cds<-vardict_cds[grep("GL*", vardict_cds$seqnames, invert=TRUE),] - colnames(vardict_cds)<-c("X.CHROM", "POS", "END_POS_Vardict", "REF_Vardict", "ALT_Vardict", "vd_SSF","vd_MSI","vd_SOR") - - #assign column and then merge with original - mutect_cds$Region <- "CDS" - mutect_cds <- mutect_cds[,c(1,2,dim(mutect_cds)[2])] - mutect_cds <- unique(mutect_cds) - mutect<-merge(mutect, mutect_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #mutect[which(is.na(mutect[,dim(mutect)[2]])), dim(mutect)[2]] <- "Non-coding" - - freebayes_cds$Region <- "CDS" - freebayes_cds <- freebayes_cds[,c(1,2,dim(freebayes_cds)[2])] - freebayes_cds <- unique(freebayes_cds) - freebayes<-merge(freebayes, freebayes_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #freebayes[which(is.na(freebayes[,dim(freebayes)[2]])), dim(freebayes)[2]] <- "Non-coding" - - varscan_cds$Region <- "CDS" - varscan_cds <- varscan_cds[,c(1,2,dim(varscan_cds)[2])] - varscan_cds <- unique(varscan_cds) - varscan<-merge(varscan, varscan_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #varscan[which(is.na(varscan[,dim(varscan)[2]])), dim(varscan)[2]] <- "Non-coding" - - vardict_cds$Region <- "CDS" - vardict_cds <- vardict_cds[,c(1,2,dim(vardict_cds)[2])] - vardict_cds <- unique(vardict_cds) - vardict<-merge(vardict, vardict_cds, by=c("X.CHROM", "POS"), all.x=TRUE, sort=TRUE) - #vardict[which(is.na(vardict[,dim(vardict)[2]])), dim(vardict)[2]] <- "Non-coding" - - - #### Coordinates filtering #### - - #Filtering SNV's from collapsed vcf - mutect_SNV<-a[[2]][isSNV(a[[2]], singleAltOnly=FALSE)] - freebayes_SNV<-a[[4]][isSNV(a[[4]], singleAltOnly=FALSE)] - varscan_SNV<-a[[6]][isSNV(a[[6]], singleAltOnly=FALSE)] - vardict_SNV<-a[[8]][isSNV(a[[8]], singleAltOnly=FALSE)] - - ## Filtering Passed calls from raw file - mutect_clean_SNV<-rowRanges(mutect_SNV[mutect_SNV@fixed$FILTER=="PASS",])[,1] - mutect_coordinates<-as.data.frame(unlist(mutect_clean_SNV),row.names=NULL) - mutect_coordinates<-mutect_coordinates[1:2] - mutect_coordinates$FILTER_Mutect2<-"PASS" - colnames(mutect_coordinates)[1:2]<-c("X.CHROM", "POS") - mutect_coordinates<-mutect_coordinates[grep("GL*", mutect_coordinates$X.CHROM, invert = TRUE),] - - freebayes_clean_SNV<-rowRanges(freebayes_SNV[freebayes_SNV@fixed$FILTER=="PASS",])[,1] - freebayes_coordinates<-as.data.frame(unlist(freebayes_clean_SNV),row.names=NULL) - freebayes_coordinates<-freebayes_coordinates[1:2] - freebayes_coordinates$FILTER_Freebayes<-"PASS" - colnames(freebayes_coordinates)[1:2]<-c("X.CHROM", "POS") - freebayes_coordinates<-freebayes_coordinates[grep("GL*", freebayes_coordinates$X.CHROM, invert = TRUE),] - - #we are including the SpvFreq as PASSED calls - varscan_clean_SNV<-rowRanges(varscan_SNV[varscan_SNV@fixed$FILTER=="PASS" | varscan_SNV@fixed$FILTER=="SpvFreq",])[,1] - varscan_coordinates<-as.data.frame(unlist(varscan_clean_SNV),row.names=NULL) - varscan_coordinates<-varscan_coordinates[1:2] - varscan_coordinates$FILTER_Varscan<-"PASS" - colnames(varscan_coordinates)[1:2]<-c("X.CHROM", "POS") - varscan_coordinates<-varscan_coordinates[grep("GL*", varscan_coordinates$X.CHROM, invert = TRUE),] - - vardict_clean_SNV<-rowRanges(vardict_SNV[vardict_SNV@fixed$FILTER=="PASS",])[,1] - vardict_coordinates<-as.data.frame(unlist(vardict_clean_SNV),row.names=NULL) - vardict_coordinates<-vardict_coordinates[1:2] - vardict_coordinates$FILTER_Vardict<-"PASS" - colnames(vardict_coordinates)[1:2]<-c("X.CHROM", "POS") - vardict_coordinates<-vardict_coordinates[grep("GL*", vardict_coordinates$X.CHROM, invert = TRUE),] - - #All Pass coordinates(i.e., coordinates passed by at least one caller) - f1<-merge(mutect_coordinates, freebayes_coordinates, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - f2<-merge(varscan_coordinates, vardict_coordinates, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - coordinates<-merge(f1, f2, by=c("X.CHROM", "POS"), all=TRUE, sort=TRUE) - coordinates<-unique(coordinates) - - #### Merge 4 callers with proper coordinates #### - - #Pulling out calls from VRanges object for each caller using coordinates - m2<-dim(mutect)[2] - mutect<-merge(mutect, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - mutect<-unique(mutect) - M_2<-which( colnames(mutect)=="FILTER_Mutect2" ) - mutect<-mutect[,c(1:m2,M_2)] - - fb<-dim(freebayes)[2] - freebayes<-merge(freebayes, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - freebayes<-unique(freebayes) - F_B<-which( colnames(freebayes)=="FILTER_Freebayes" ) - freebayes<-freebayes[,c(1:fb,F_B)] - - vs<-dim(varscan)[2] - varscan<-merge(varscan, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - varscan<-unique(varscan) - V_S<-which( colnames(varscan)=="FILTER_Varscan" ) - varscan<-varscan[,c(1:vs,V_S)] - - vd<-dim(vardict)[2] - vardict<-merge(vardict, coordinates, by=c("X.CHROM", "POS"), all.y=TRUE, sort=TRUE) - vardict<-unique(vardict) - V_D<-which( colnames(vardict)=="FILTER_Vardict" ) - vardict<-vardict[,c(1:vd,V_D)] - - #Merging all calls from each caller - f1<-merge(mutect, freebayes, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - f2<-merge(varscan, vardict, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - - final<-merge(f1,f2, by = c("X.CHROM", "POS", "Region"), all=TRUE, sort=TRUE) - final[which(is.na(final[,c("Region")])), c("Region")] <- "Non-coding" - - raw <- final - - #Formatting - final$REF<-paste(final$REF_Mutect2,final$REF_Freebayes,final$REF_Vardict,final$REF_Varscan, sep ="/") - final$ALT<-paste(final$ALT_Mutect2,final$ALT_Freebayes,final$ALT_Vardict,final$ALT_Varscan, sep ="/") - f<-subset(final,select=c("END_POS_Mutect2", "END_POS_Freebayes", "END_POS_Vardict", "END_POS_Varscan")) - final$END_POS<-apply(f, MARGIN=1, function(x) max(x,na.rm=TRUE)) - final<-final[,c("X.CHROM", "POS", "END_POS", "REF", "ALT", "Region", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD", - "f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP", - "vs_SSC","vs_GPV","vs_SS","vs_SPV","vd_SSF","vd_MSI","vd_SOR")] - colnames(final)<-c("X.CHROM", "START_POS_REF", "END_POS_REF", "REF_MFVdVs", "ALT_MFVdVs", "REGION", "FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan", - "m2_BaseQRankSum","m2_ClippingRankSum","m2_FS","m2_HCNT","m2_MQ","m2_MQRankSum","m2_NLOD","m2_ReadPosRankSum","m2_TLOD", - "f_AB","f_ABP","f_EPP","f_EPPR","f_GTI","f_LEN","f_MQM","f_MQMR","f_NS","f_NUMALT","f_ODDS","f_PAIRED","f_PAIREDR","f_RPP","f_SAP","f_SRP", - "vs_SSC","vs_GPV","vs_SS","vs_SPV","vd_SSF","vd_MSI","vd_SOR") - - for(i in 11:dim(final)[2]) - { - final[,i]<-as.numeric(final[,i]) - } - - - #Removing Duplicates - final<-unique(final) - - for(i in c("FILTER_Mutect2", "FILTER_Freebayes", "FILTER_Vardict", "FILTER_Varscan")) - { - final[which(is.na(final[,i])), i] <- FALSE - final[which(final[,i]!="PASS"), i] <- "FALSE" - final[which(final[,i]=="PASS"), i] <- "TRUE" - final[,i] <- as.logical(final[,i]) - } - - final$vd_SOR[which(is.infinite(final$vd_SOR)==TRUE)] <- 0 - - #df <- final[,c(1:2,6:dim(final)[2])] - #write.csv(df, 'snv_parse.csv',row.names = F) - #df <- h2o.importFile(path = normalizePath("snv_parse.csv"),header=T) - - final<-as.matrix(final) - y <- list(final) - names(y)<- c("allfeatures_snv") - return(y) - - - #write.table(final , file = "snv-parse-allfeatures.txt", sep = "\t", quote = FALSE, row.names = FALSE) - #x = read.table('snv-parse-allfeatures.txt',header=T,sep = "\t") - #write.csv(x, 'snv-parse-allfeatures.csv',row.names = F) - - -} diff --git a/smurf/data/indel-model-combined-grid b/smurf/data/indel-model-combined-grid index ce691a9..f3cba14 100644 Binary files a/smurf/data/indel-model-combined-grid and b/smurf/data/indel-model-combined-grid differ diff --git a/smurf/data/snv-model-combined-grid b/smurf/data/snv-model-combined-grid index 0c51541..5d82ce1 100644 Binary files a/smurf/data/snv-model-combined-grid and b/smurf/data/snv-model-combined-grid differ diff --git a/smurf/man/parsevcf.Rd b/smurf/man/parsevcf.Rd index 966a65c..17c17c9 100644 --- a/smurf/man/parsevcf.Rd +++ b/smurf/man/parsevcf.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/parsevcf.R \name{parsevcf} \alias{parsevcf} -\title{parse} +\title{parsevcf} \usage{ parsevcf(x) } diff --git a/smurf/man/smurf.Rd b/smurf/man/smurf.Rd index a302337..48cc131 100644 --- a/smurf/man/smurf.Rd +++ b/smurf/man/smurf.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/smurf.R \name{smurf} \alias{smurf} -\title{SMuRF} +\title{SMuRF v1.1} \usage{ smurf(directory, model) } diff --git a/smurf/smurf.Rproj b/smurf/smurf.Rproj deleted file mode 100644 index 50ef3cc..0000000 --- a/smurf/smurf.Rproj +++ /dev/null @@ -1,16 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: No -SaveWorkspace: No -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -Encoding: UTF-8 - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd,collate,namespace diff --git a/test/results/indel-parse.txt b/test/results/indel-parse.txt index 1b53b22..cd1f9c3 100644 --- a/test/results/indel-parse.txt +++ b/test/results/indel-parse.txt @@ -1,766 +1,811 @@ -X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs FILTER_Mutect2 FILTER_Freebayes FILTER_Vardict FILTER_Varscan m2_MQ m2_MQRankSum m2_NLOD m2_TLOD f_LEN vs_SSC vs_SPV vd_SSF vd_MSI -1 1 100202139 100202139 C/NA/NA/NA CTTAAAAAAATA/NA/NA/NA TRUE FALSE FALSE FALSE 59.29 0.449 5.74 6.44 . . . . . -2 1 10022735 10022736 NA/GT/NA/G NA/G/NA/GT FALSE FALSE FALSE TRUE . . . . 1 14 3.5518e-02 . . -3 1 10022735 10022736 NA/GT/NA/G NA/GTT/NA/GT FALSE FALSE FALSE TRUE . . . . 1 14 3.5518e-02 . . -4 1 10041925 10041926 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 13 4.9053e-02 . . -5 1 100448319 100448319 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 12.22 . . . . . -6 1 100448320 100448320 G/NA/NA/NA GATATACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 12.22 . . . . . -7 1 101241945 101241945 A/NA/NA/NA AAAGTCATATGACTCACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.78 9.21 . . . . . -8 1 101273498 101273498 A/NA/NA/NA ATCACTTGCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.65 11.94 . . . . . -9 1 101273500 101273500 T/NA/NA/NA TAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.63 11.95 . . . . . -10 1 101338625 101338625 T/NA/NA/NA TAGGCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 9.17 . . . . . -11 1 101386745 101386749 TAGAG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.02 . . . . . -12 1 1014360 1014361 NA/NA/GG/NA NA/NA/CC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.26520 6.00 -13 1 101525739 101525739 A/NA/NA/NA ACCAGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.84 12.40 . . . . . -14 1 10179 10179 NA/NA/NA/C NA/NA/NA/CCT FALSE FALSE FALSE TRUE . . . . . 3 4.0441e-01 . . -15 1 10210 10211 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 3 4.3590e-01 . . -16 1 102315720 102315720 A/NA/NA/NA AGTTATGCTTC/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.000 8.80 8.74 . . . . . -17 1 102327622 102327622 A/NA/NA/NA AATGTTGAAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 8.71 . . . . . -18 1 102513289 102513289 G/NA/NA/NA GTTGGGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.98 9.82 . . . . . -19 1 102572520 102572520 G/NA/NA/NA GGCTAAGATCAAGTATAGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.46 9.26 . . . . . -20 1 10267337 10267337 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 13 4.3453e-02 . . -21 1 1028417 1028418 NA/NA/CA/CA NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 17 1.7767e-02 0.00440 11.00 -22 1 103307408 103307408 G/NA/NA/NA GGTTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 9.69 . . . . . -23 1 1034532 1034535 NA/NA/NA/CTAT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.7368e-02 . . -24 1 10351 10351 NA/NA/NA/C NA/NA/NA/CG FALSE FALSE FALSE TRUE . . . . . 10 9.9617e-02 . . -25 1 103641570 103641570 A/NA/NA/NA ACGTCAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.12 9.32 . . . . . -26 1 10366815 10366815 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 7 1.6221e-01 . . -27 1 103774297 103774297 A/NA/NA/NA AATAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.69 . 14.33 12.04 . . . . . -28 1 103784492 103784492 T/NA/NA/NA TTAACACTTCGATCAGTGAGAATACC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.48 8.73 . . . . . -29 1 104033649 104033651 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.24 6.76 . . . . . -30 1 10408837 10408838 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -31 1 104134500 104134500 A/NA/NA/NA AGAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.61 7.93 . . . . . -32 1 10469706 10469706 NA/NA/C/NA NA/NA/CTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00004 33.00 -33 1 104809335 104809335 A/NA/NA/NA AACTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 8.80 . . . . . -34 1 104910369 104910369 T/NA/NA/NA TGCAGAATAAACAAGTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.32 11.90 . . . . . -35 1 10491895 10491895 NA/A/A/A NA/AGCGAGACTCC/AGCGAGACTCC/AGCGAGACTCC FALSE TRUE FALSE TRUE . . . . 10 22 5.3875e-03 0.85482 2.00 -36 1 10495773 10495773 T/NA/NA/NA TACACACACACACACACAC/NA/NA/NA TRUE FALSE FALSE FALSE 59.81 . 6.29 6.37 . . . . . -37 1 105110948 105110948 C/NA/NA/NA CTATTAAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.69 9.63 . . . . . -38 1 105381264 105381264 T/NA/NA/NA TATGTGGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.42 9.01 . . . . . -39 1 105461037 105461037 A/NA/NA/NA ATATGTTT/NA/NA/NA TRUE FALSE FALSE FALSE 59.79 0.263 11.74 8.84 . . . . . -40 1 105497136 105497136 A/NA/NA/NA ATAATGATTTAGAATTTTAGGAAAATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.04 9.09 . . . . . -41 1 105687075 105687075 A/NA/NA/NA ATTGTTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.08 9.05 . . . . . -42 1 10606761 10606762 NA/GA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -43 1 106342981 106342981 T/NA/NA/NA TTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 8.77 . . . . . -44 1 1066810 1066810 NA/NA/C/NA NA/NA/CTTTTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 20.00 -45 1 106845263 106845263 T/NA/NA/NA TACTTAAGGAATTGCAAATTAAAATAACCCATAAGATACTATTATATACTTATTAGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.71 9.21 . . . . . -46 1 10718053 10718054 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 8 1.3663e-01 . . -47 1 107922569 107922569 A/NA/NA/NA AGTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.26 . . . . . -48 1 108231459 108231459 A/NA/NA/NA AACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.46 8.84 . . . . . -49 1 108430247 108430254 AATCTTTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.12 9.47 . . . . . -50 1 10854233 10854235 NA/CGT/NA/CGT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 2 5 2.5692e-01 . . -51 1 10857307 10857308 NA/TG/TG/TG NA/T/T/T FALSE FALSE TRUE TRUE . . . . 1 10 8.9571e-02 0.14923 10.00 -52 1 10877986 10877986 NA/NA/T/NA NA/NA/TTCTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 5.00 -53 1 109053538 109053538 C/NA/NA/NA CTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.16 9.26 . . . . . -54 1 109317925 109317925 A/NA/NA/NA AGAATTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 8.88 . . . . . -55 1 10943746 10943746 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.93 6.75 . . . . . -56 1 10943747 10943747 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.93 6.74 . . . . . -57 1 110447824 110447827 CTAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.57 6.70 . . . . . -58 1 11068690 11068694 CATAA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.78 7.50 . . . . . -59 1 11094454 11094455 NA/NA/TA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03863 12.00 -60 1 11099792 11099792 NA/NA/G/NA NA/NA/GA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02825 2.00 -61 1 11101803 11101803 NA/NA/G/NA NA/NA/GTGGATGGATAGATAGATGGCTGGAAGGATGGATTAATGGGTGGATTGATGGATGGGTAGGATTGGTAGGTAGAAGGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00043 3.00 -62 1 11138321 11138322 NA/CT/CT/CT NA/C/C/C FALSE TRUE TRUE TRUE . . . . 1 15 2.6475e-02 0.00288 11.00 -63 1 112091829 112091829 G/NA/NA/NA GATAAGGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.57 9.22 . . . . . -64 1 11427605 11427605 NA/A/A/NA NA/AT/AT/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.28547 12.00 -65 1 11433951 11433951 NA/G/NA/NA NA/GAT/NA/NA FALSE TRUE FALSE FALSE . . . . 2 . . . . -66 1 11434412 11434412 NA/NA/T/NA NA/NA/TGGTGTGTGTGGTGTGTGGATGATGGATGTGTGTGGATATGGATGTGTGTGGTGTGTGGATATGGATGTGTGTGGTGCATGGATATG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00546 3.00 -67 1 114350395 114350397 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 12.79 . . . . . -68 1 11499557 11499559 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.13 5.773 14.71 6.91 . . . . . -69 1 115228332 115228332 A/NA/NA/NA AATCAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.10 9.09 . . . . . -70 1 115403519 115403519 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.02 . . . . . -71 1 115403520 115403520 A/NA/NA/NA ATACATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.02 . . . . . -72 1 115403968 115403968 T/NA/NA/NA TAACTATAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.53 9.17 . . . . . -73 1 116811095 116811095 T/NA/NA/NA TGCCCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 30.43 7.09 . . . . . -74 1 11700567 11700568 NA/TA/TA/TA NA/T/T/T FALSE FALSE FALSE TRUE . . . . 1 13 4.1862e-02 0.02975 9.00 -75 1 11726441 11726441 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 20 8.3090e-03 . . -76 1 11734353 11734353 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 59.58 -12.381 26.09 9.98 . . . . . -77 1 118975114 118975114 G/NA/NA/NA GAGAAAGAGCGTCGTGTAGGGAAAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 6.31 . . . . . -78 1 11906676 11906676 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 26 2.1245e-03 . . -79 1 11967783 11967783 NA/T/NA/NA NA/TA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -80 1 119930379 119930379 A/NA/NA/NA AGTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.31 . . . . . -81 1 12021148 12021149 NA/NA/TA/TA NA/NA/T/T FALSE FALSE TRUE TRUE . . . . . 13 4.7727e-02 0.01001 10.00 -82 1 12041977 12041977 NA/G/G/NA NA/GT/GTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00033 21.00 -83 1 12041977 12041977 NA/G/G/NA NA/GTTTTTTT/GTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 7 . . 0.00033 21.00 -84 1 12057936 12057936 NA/NA/C/NA NA/NA/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 28.00 -85 1 12076969 12076969 NA/G/G/NA NA/GTT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 25.00 -86 1 12076969 12076969 NA/G/G/NA NA/GTTT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 25.00 -87 1 12076969 12076969 NA/G/G/NA NA/GT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 25.00 -88 1 12122588 12122588 NA/G/G/NA NA/GCATCCATC/GCATCCATC/NA FALSE FALSE TRUE FALSE . . . . 8 . . 0.01003 10.00 -89 1 1224359 1224359 NA/NA/T/T NA/NA/TCC/TCC FALSE FALSE FALSE TRUE . . . . . 4 3.2903e-01 0.22794 5.00 -90 1 122949 122949 C/NA/NA/NA CAAAAGTT/NA/NA/NA TRUE FALSE FALSE FALSE 42.38 -2.615 4.21 6.44 . . . . . -91 1 12349620 12349620 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -92 1 12387978 12387979 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02444 11.00 -93 1 12408687 12408688 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.07857 11.00 -94 1 12426122 12426122 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 5 2.5714e-01 . . -95 1 12439825 12439826 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -96 1 12494025 12494028 NA/TGGA/TGGA/TGGA NA/T/T/T FALSE FALSE TRUE FALSE . . . . 3 23 4.5928e-03 0.00001 10.00 -97 1 12494025 12494028 NA/TGGA/TGGA/TGGA NA/TGA/T/T FALSE FALSE TRUE FALSE . . . . 1 23 4.5928e-03 0.00001 10.00 -98 1 12509191 12509191 NA/G/NA/NA NA/GA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -99 1 12509450 12509450 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -100 1 12519537 12519538 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 14 3.7726e-02 . . -101 1 12589073 12589074 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -102 1 12635723 12635726 CTAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.29 8.83 . . . . . -103 1 12783857 12783857 NA/A/A/NA NA/ACTTCTGCCTCCTGGGTTCAAGGGATT/ACTTCAGCCTCCTGGGTTCAAGGGATT/NA FALSE FALSE TRUE FALSE . . . . 26 . . 0.05952 2.00 -104 1 12800857 12800859 NA/CTT/C/NA NA/CTTTTT/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 25.00 -105 1 12800857 12800859 NA/CTT/C/NA NA/C/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 25.00 -106 1 12891724 12891744 NA/NA/CACCTGAAACCCAGCTACATG/NA NA/NA/GGCCTGAAACACAGCGACTCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00003 4.00 -107 1 13007229 13007229 NA/NA/G/NA NA/NA/GA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02121 11.00 -108 1 13051050 13051050 C/NA/NA/NA CACTAGT/NA/NA/NA TRUE FALSE FALSE FALSE 47.09 -1.648 5.75 10.15 . . . . . -109 1 13116353 13116353 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 11 6.9231e-02 . . -110 1 13155619 13155619 G/NA/NA/NA GCATCTACT/NA/NA/NA TRUE FALSE FALSE FALSE 47.62 -0.424 15.01 8.65 . . . . . -111 1 13168951 13168951 NA/G/G/G NA/GAAGAAAGAAAGA/GAAGAAAGAAAGA/GAAGAAAGAAAGA FALSE FALSE FALSE TRUE . . . . 12 14 3.7589e-02 0.02447 16.00 -112 1 13168951 13168951 NA/G/G/G NA/GAAGA/GAAGAAAGAAAGA/GAAGAAAGAAAGA FALSE FALSE FALSE TRUE . . . . 4 14 3.7589e-02 0.02447 16.00 -113 1 13177471 13177471 NA/C/C/NA NA/CT/CT/NA FALSE TRUE TRUE FALSE . . . . 1 . . 0.10264 11.00 -114 1 1318005 1318005 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 9 1.1029e-01 . . -115 1 13774646 13774646 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -116 1 13775521 13775522 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -117 1 13805627 13805627 NA/C/C/C NA/CT/CT/CT FALSE FALSE FALSE TRUE . . . . 1 9 1.2195e-01 0.10638 11.00 -118 1 13926866 13926866 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -119 1 14034316 14034317 NA/CT/NA/CT NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 14 3.5782e-02 . . -120 1 14126948 14126950 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 6.38 . . . . . -121 1 142550392 142550392 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 48.67 -0.834 33.09 11.88 . . . . . -122 1 142581125 142581127 GTT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 49.52 -3.580 11.47 6.55 . . . . . -123 1 14262591 14262591 NA/G/G/NA NA/GTTTTTTTTTTT/GTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 11 . . 0.00009 27.00 -124 1 14262591 14262591 NA/G/G/NA NA/GTTTTTTTTTTTT/GTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 12 . . 0.00009 27.00 -125 1 142670528 142670530 ACT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 47.29 -1.830 5.89 33.53 . . . . . -126 1 142918207 142918208 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 46.27 0.133 8.03 7.83 . . . . . -127 1 143135392 143135393 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 52.26 -3.070 24.02 12.48 . . . . . -128 1 143151982 143151982 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 53.40 -2.839 4.37 11.38 . . . . . -129 1 143158449 143158449 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 53.10 -2.608 67.57 16.69 . . . . . -130 1 143168922 143168965 ACCTTACTGACAAGGCCTCACTGGCAAGGCCTCACTGACGAGGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.33 -2.220 33.40 7.18 . . . . . -131 1 14329215 14329215 C/NA/NA/NA CTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.94 8.84 . . . . . -132 1 143428977 143428977 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 42.35 -1.571 3.93 13.78 . . . . . -133 1 143482108 143482109 TC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 46.94 -2.025 3.69 24.59 . . . . . -134 1 143504763 143504763 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 48.42 -0.660 8.88 7.43 . . . . . -135 1 144579868 144579868 A/NA/NA/NA AATGT/NA/NA/NA TRUE FALSE FALSE FALSE 47.59 -2.513 7.22 6.83 . . . . . -136 1 144602222 144602222 C/NA/NA/NA CATAAGAATCCTAAGAGA/NA/NA/NA TRUE FALSE FALSE FALSE 44.21 -1.394 3.04 6.44 . . . . . -137 1 144899410 144899410 G/NA/NA/NA GTTTTTTATATAGT/NA/NA/NA TRUE FALSE FALSE FALSE 59.82 -8.619 11.18 8.91 . . . . . -138 1 144991389 144991397 TACACACAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 57.56 2.427 7.17 21.71 . . . . . -139 1 145016034 145016034 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.04 0.000 7.58 30.52 . . . . . -140 1 145037620 145037620 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 59.38 -1.584 22.83 6.52 . . . . . -141 1 145040832 145040832 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.95 11.19 . . . . . -142 1 145110305 145110305 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 36.75 10.05 . . . . . -143 1 145110306 145110306 A/NA/NA/NA AAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 36.74 10.05 . . . . . -144 1 145236043 145236049 AGTGTTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 56.06 -3.365 19.81 7.08 . . . . . -145 1 145250219 145250219 A/NA/NA/NA ATATT/NA/NA/NA TRUE FALSE FALSE FALSE 57.83 -3.866 10.09 8.45 . . . . . -146 1 145292407 145292408 AC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.91 3.299 11.41 39.80 . . . . . -147 1 145375050 145375050 C/NA/NA/NA CAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 50.92 -1.251 13.98 7.14 . . . . . -148 1 145376566 145376566 T/NA/NA/NA TC/NA/NA/NA TRUE FALSE FALSE FALSE 53.17 -3.235 19.71 9.14 . . . . . -149 1 1454046 1454048 NA/TAC/TAC/NA NA/T/T/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.51471 12.00 -150 1 146397483 146397483 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 53.31 -4.536 7.53 10.37 . . . . . -151 1 146479610 146479610 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 57.38 -7.337 6.77 12.40 . . . . . -152 1 14662242 14662244 NA/NA/GCA/NA NA/NA/G/NA FALSE FALSE TRUE FALSE . . . . . . . 0.11412 7.00 -153 1 14671412 14671413 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -154 1 147025524 147025524 A/NA/NA/NA AGCTAATATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.47 8.97 . . . . . -155 1 147311506 147311521 TATATGTGAGACATAG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 55.29 -5.289 7.23 6.51 . . . . . -156 1 147343502 147343502 G/NA/NA/NA GTGTTCTACAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.24 12.65 . . . . . -157 1 147356904 147356904 C/NA/NA/NA CCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.64 12.88 . . . . . -158 1 148001285 148001285 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 51.20 0.392 16.90 11.21 . . . . . -159 1 148352296 148352298 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.41 0.000 4.41 14.39 . . . . . -160 1 148849102 148849128 TCATTTCATTTCCTCATTTCATTTCAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 53.68 0.587 3.56 28.85 . . . . . -161 1 148849397 148849402 ACATTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 51.79 -3.993 29.69 28.14 . . . . . -162 1 149338550 149338550 T/NA/NA/NA TGTGTTAGTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 54.30 -3.043 10.23 6.65 . . . . . -163 1 14949185 14949186 NA/CA/C/NA NA/C/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 0.00 -164 1 14949185 14949186 NA/CA/C/NA NA/CAAAAAAAA/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 7 . . 0.00000 0.00 -165 1 149857497 149857497 A/NA/NA/NA AATAATCCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 -0.099 15.09 7.80 . . . . . -166 1 149857499 149857499 G/NA/NA/NA GCACTTTGAGAGACCAAGGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 -0.099 15.09 7.80 . . . . . -167 1 149879052 149879066 ATATTCTATTACAGG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.38 8.69 . . . . . -168 1 1501010 1501010 NA/NA/G/NA NA/NA/GTGGGCTCCATGGGAACCGAGACCCAACACCCAAAGGAGTCCCACAGGCTCAGGGGTGGTGCAGGCAGAGAACAGACGTCGCGATGGGCCCGACGGTGC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -169 1 150256413 150256416 TTTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.280 9.63 19.03 . . . . . -170 1 150356926 150356932 CATTATT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 . 12.76 7.67 . . . . . -171 1 150360955 150360957 CTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.95 8.94 . . . . . -172 1 15062748 15062748 NA/NA/A/A NA/NA/AGG/AGG FALSE FALSE FALSE TRUE . . . . . 10 9.5238e-02 0.57946 5.00 -173 1 15089357 15089360 CAAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.76 10.77 . . . . . -174 1 150908053 150908053 C/NA/NA/NA CCTCGGCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 8.83 . . . . . -175 1 15116656 15116656 T/NA/NA/NA TCTGTAATGATACCCACAGACTCAAAGTAAAAGGATGGAGAAAGGTTTG/NA/NA/NA TRUE FALSE FALSE FALSE 59.59 0.000 16.56 6.37 . . . . . -176 1 151326041 151326041 G/NA/NA/NA GACCA/NA/NA/NA TRUE FALSE FALSE FALSE 59.47 -7.093 12.05 10.57 . . . . . -177 1 15176434 15176435 NA/CT/CT/CT NA/C/C/C FALSE TRUE FALSE FALSE . . . . 1 21 7.0648e-03 0.00184 14.00 -178 1 152106280 152106281 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.53 7.52 . . . . . -179 1 15236546 15236546 NA/C/C/C NA/CAATA/CAATA/CAATA FALSE FALSE TRUE TRUE . . . . 4 22 5.4987e-03 0.00704 4.00 -180 1 152863578 152863581 AAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.85 10.54 . . . . . -181 1 152974408 152974408 G/NA/NA/NA GTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 13.23 . . . . . -182 1 152989728 152989728 T/NA/NA/NA TATATACGTGTATATATATATACATATACACGTATATACGTGTATATATATACATATACACGTATATACGTGTATATATATATAC/NA/NA/NA TRUE FALSE FALSE FALSE 57.02 -4.628 3.87 14.24 . . . . . -183 1 15319663 15319664 NA/TA/NA/TA NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 1 18 1.4475e-02 . . -184 1 15332287 15332288 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -185 1 153861447 153861447 A/NA/NA/NA AACTACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.06 9.45 . . . . . -186 1 15427660 15427660 NA/T/T/T NA/TTCTCTCTCTC/TTCTCTCTCTCTCTCTCTCTCTCTC/TTCTCTCTCTC FALSE FALSE TRUE FALSE . . . . 10 1 7.4954e-01 0.00004 23.00 -187 1 154331579 154331581 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.13 6.33 . . . . . -188 1 154357184 154357188 AAAAC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.70 6.33 . . . . . -189 1 154694454 154694454 G/NA/NA/NA GAGCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 16.26 9.01 . . . . . -190 1 155095812 155095815 CTTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.12 11.21 . . . . . -191 1 15554510 15554512 NA/NA/NA/TTG NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 12 6.1668e-02 . . -192 1 155634552 155634552 A/NA/NA/NA AGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.36 . . . . . -193 1 155634553 155634553 A/NA/NA/NA AGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.36 . . . . . -194 1 15572956 15572979 NA/NA/AGATAGGATTTCCTGCTGGAGATA/NA NA/NA/TTGCTCTGCCCTCAAGTAGAAGTGGGAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -195 1 15598102 15598102 NA/NA/T/NA NA/NA/TGGAAATAACTAATCGCATG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00042 3.00 -196 1 15629213 15629214 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -197 1 15635778 15635782 GATTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.49 6.45 . . . . . -198 1 15641171 15641171 NA/NA/T/NA NA/NA/TGGGTGTAAGCATAGGGGGTGTATGGGTGTGAGTATGGGGGGAGTATGTATGGGTGTGTGGGGTGTGTGTGGATGTGTGGGTGAGGGTGTTGGGAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -199 1 15641246 15641246 NA/NA/G/NA NA/NA/GTGGATGTGTGTGGGTATGTGGGGGGTGTGGGAGTGTGGAGATGTATGAGTGTGGGTGTGTGAGAGGGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00238 4.00 -200 1 156682152 156682154 GGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.54 6.84 . . . . . -201 1 15710494 15710496 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 26.62 9.04 . . . . . -202 1 157761187 157761187 G/NA/NA/NA GCTGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 15.84 . . . . . -203 1 15781658 15781658 NA/A/A/NA NA/AC/AC/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 40.00 -204 1 15781702 15781703 NA/NA/NA/TC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 9 1.1565e-01 . . -205 1 15790384 15790385 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -206 1 157966837 157966845 GACTAAGTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 28.28 7.42 . . . . . -207 1 15821357 15821358 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 18 1.3082e-02 . . -208 1 158675701 158675701 A/NA/NA/NA AGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.51 8.84 . . . . . -209 1 158685987 158685987 T/NA/NA/NA TGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.23 9.09 . . . . . -210 1 158839725 158839725 G/NA/NA/NA GCTA/NA/NA/NA TRUE FALSE FALSE FALSE 58.77 -4.900 12.64 6.33 . . . . . -211 1 158871726 158871726 T/NA/NA/NA TTTTCGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 12.71 . . . . . -212 1 15896892 15896892 G/NA/NA/NA GCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 9.36 . . . . . -213 1 15913105 15913106 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 13 4.4382e-02 . . -214 1 159387827 159387828 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.60 52.16 . . . . . -215 1 1594841 1594841 NA/NA/A/NA NA/NA/CTCGACGGGGAGGTGGACAAGG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -216 1 159622056 159622058 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 10.35 . . . . . -217 1 160222308 160222308 T/NA/NA/NA TAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.14 12.88 . . . . . -218 1 16024292 16024293 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.12354 12.00 -219 1 160247155 160247166 AGCACACAGTGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.46 9.10 . . . . . -220 1 160991956 160991960 ATTGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 20.40 7.75 . . . . . -221 1 160993666 160993666 C/NA/NA/NA CTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.39 -0.313 15.79 8.05 . . . . . -222 1 161414339 161414341 GTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 36.25 -0.848 3.49 22.15 . . . . . -223 1 16155538 16155539 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 2.5348e-02 . . -224 1 161664777 161664777 T/NA/NA/NA TCCCCG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.17 9.05 . . . . . -225 1 1616853 1616853 NA/NA/G/G NA/NA/AAAA/GA FALSE FALSE TRUE FALSE . . . . . 4 3.2372e-01 0.00026 0.00 -226 1 16187104 16187104 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 13 3.9989e-02 . . -227 1 16191915 16191917 NA/GTT/NA/G NA/GTTT/NA/GT FALSE FALSE FALSE TRUE . . . . 1 13 4.4097e-02 . . -228 1 16191915 16191917 NA/GTT/NA/G NA/G/NA/GT FALSE FALSE FALSE TRUE . . . . 2 13 4.4097e-02 . . -229 1 16218507 16218508 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 3.0302e-02 . . -230 1 16218507 16218508 NA/CT/NA/CT NA/CTT/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 3.0302e-02 . . -231 1 16231386 16231387 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -232 1 162493357 162493357 G/NA/NA/NA GCATACAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 9.25 . . . . . -233 1 162782394 162782394 G/NA/NA/NA GTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 59.49 -7.809 14.45 6.44 . . . . . -234 1 16293437 16293437 NA/NA/C/NA NA/NA/CA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02372 11.00 -235 1 16297851 16297851 NA/NA/C/NA NA/NA/CACACTATATATATAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.08904 5.00 -236 1 16308412 16308412 NA/NA/A/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00008 0.00 -237 1 163177630 163177630 A/NA/NA/NA ATGACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 6.57 . . . . . -238 1 163239608 163239609 AT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.82 9.38 . . . . . -239 1 163681702 163681702 A/NA/NA/NA ATGTGGTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.57 12.99 . . . . . -240 1 163681703 163681703 A/NA/NA/NA AATTTGTATTTTTCTGATGATAGTGATGGTTGAGTATCTTTTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.57 12.99 . . . . . -241 1 16382828 16382834 NA/NA/TCTTCCT/NA NA/NA/ACCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00142 4.00 -242 1 16388757 16388766 NA/NA/ACCCATCCCC/NA NA/NA/CCCT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00006 6.00 -243 1 164128083 164128084 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.73 6.80 . . . . . -244 1 164145929 164145930 GT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.83 -0.393 8.97 49.45 . . . . . -245 1 164349942 164349942 A/NA/NA/NA ACATATCCCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.55 9.09 . . . . . -246 1 1643570 1643572 NA/NA/NA/CAA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 4 3.3088e-01 . . -247 1 164621971 164621971 A/NA/NA/NA AAAATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 9.26 . . . . . -248 1 164621972 164621972 C/NA/NA/NA CCAATAATATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 9.26 . . . . . -249 1 164885488 164885488 C/NA/NA/NA CCAAAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.75 13.08 . . . . . -250 1 1649112 1649163 NA/NA/GCTCTCTCTGGTTTTCGGTCTGTGACACACGCACACTTTCAGCTGGAGTATC/NA NA/NA/G/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00583 2.00 -251 1 1651074 1651077 NA/NA/AGAC/NA NA/NA/TAAACCCGCTCTGTCACCCAGGCT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 19.00 -252 1 16517823 16517825 NA/NA/NA/GGA NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 6 2.1429e-01 . . -253 1 165832980 165832980 G/NA/NA/NA GAAACAATAATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.38 8.87 . . . . . -254 1 16636855 16636856 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.32524 11.00 -255 1 16668104 16668105 NA/TA/NA/TA NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 1 19 1.0366e-02 . . -256 1 16697888 16697902 CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG C/C/C/C TRUE TRUE FALSE TRUE 58.21 2.381 3.54 26.86 14 16 2.5045e-02 0.00000 4.00 -257 1 16776783 16776783 NA/NA/NA/G NA/NA/NA/GT FALSE FALSE FALSE TRUE . . . . . 7 1.6944e-01 . . -258 1 167871740 167871740 G/NA/NA/NA GACCTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.85 9.09 . . . . . -259 1 167965998 167965998 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 8.94 . . . . . -260 1 167966000 167966001 GC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.94 8.94 . . . . . -261 1 16840566 16840566 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 55.98 -1.492 13.04 17.04 . . . . . -262 1 16842744 16842745 GC/NA/NA/GC G/NA/NA/G FALSE FALSE FALSE TRUE 56.43 -0.750 34.13 25.24 . 14 3.9759e-02 . . -263 1 16849776 16849778 CCA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 56.32 -9.856 8.77 7.36 . . . . . -264 1 169029403 169029403 C/NA/NA/NA CTTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.26 6.83 . . . . . -265 1 169209503 169209503 G/NA/NA/NA GTTTGAGAACTTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 9.57 . . . . . -266 1 16923136 16923138 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 59.45 -6.397 40.97 7.28 . . . . . -267 1 16933623 16933628 NA/GAAGAA/GAAGAA/GAAGAA NA/G/G/G FALSE FALSE FALSE TRUE . . . . 5 18 1.4683e-02 0.05902 4.00 -268 1 16955682 16955693 NA/ATTTTTTTTTTT/A/ATTTTTTTTTTT NA/A/ATTTTTTTTTT/A FALSE FALSE TRUE FALSE . . . . 11 0 8.4047e-01 0.00000 31.00 -269 1 16955682 16955693 NA/ATTTTTTTTTTT/A/ATTTTTTTTTTT NA/ATTTTTTTTTTTT/ATTTTTTTTTT/A FALSE FALSE TRUE FALSE . . . . 1 0 8.4047e-01 0.00000 31.00 -270 1 16965863 16965863 NA/NA/NA/A NA/NA/NA/ACAGCAG FALSE FALSE FALSE TRUE . . . . . 14 3.8507e-02 . . -271 1 16970870 16970870 G/NA/G/G GC/NA/GC/GC FALSE FALSE FALSE TRUE 59.77 0.696 2.76 21.32 . 15 2.9144e-02 0.21744 4.00 -272 1 16978192 16978193 AC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 57.64 -2.826 6.84 14.93 . . . . . -273 1 169883560 169883560 A/NA/NA/NA AATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.55 9.09 . . . . . -274 1 17007961 17007961 NA/A/NA/A NA/AC/NA/AC FALSE FALSE FALSE TRUE . . . . 1 16 2.4913e-02 . . -275 1 170215106 170215106 T/NA/NA/NA TTATATATTTTAGTTATTAACC/NA/NA/NA TRUE FALSE FALSE FALSE 59.45 0.000 5.20 9.51 . . . . . -276 1 17030009 17030011 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.02 -0.168 34.59 11.80 . . . . . -277 1 17034808 17034808 NA/NA/C/NA NA/NA/CTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 32.00 -278 1 17051738 17051747 NA/CAGCTTCTGG/CAGCTTCTGG/CAGCTTCTGG NA/C/C/C FALSE TRUE FALSE FALSE . . . . 9 102 5.0170e-11 0.30992 2.00 -279 1 17053771 17053774 NA/NA/NA/TGTG NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 29 1.0966e-03 . . -280 1 170586144 170586144 A/NA/NA/NA ATACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.96 9.22 . . . . . -281 1 17060199 17060200 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 38.22 -1.631 12.93 31.02 . . . . . -282 1 170672812 170672812 T/NA/NA/NA TCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.05 9.05 . . . . . -283 1 170700350 170700350 C/NA/NA/NA CCTCTTGTATCTTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.18 . . . . . -284 1 17084729 17084730 CG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 52.31 0.315 18.45 8.14 . . . . . -285 1 17190073 17190074 NA/NA/CT/NA NA/NA/TC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00149 1.00 -286 1 171950789 171950789 G/NA/NA/NA GAGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 9.09 . . . . . -287 1 171968245 171968245 G/NA/NA/NA GGGCCCCTTTCAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 9.26 . . . . . -288 1 17202553 17202561 GTTTGTTTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 55.99 -3.068 3.35 28.43 . . . . . -289 1 17217939 17217941 NA/NA/NA/TTC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 40 9.7149e-05 . . -290 1 172221200 172221200 T/NA/NA/NA TCTGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.95 8.54 . . . . . -291 1 172508758 172508758 A/NA/NA/NA AAGAGATTTCATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.40 8.60 . . . . . -292 1 172555560 172555560 G/NA/NA/NA GAAAGTAATATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.31 6.51 . . . . . -293 1 172809799 172809801 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.10 6.64 . . . . . -294 1 173121421 173121423 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.66 7.04 . . . . . -295 1 17325900 17325901 NA/AG/AG/NA NA/A/A/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00007 25.00 -296 1 173354278 173354278 T/NA/NA/NA TAAAAATTTATATTTAACATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.87 9.13 . . . . . -297 1 17358699 17358700 NA/CT/NA/CT NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 16 2.2127e-02 . . -298 1 173630187 173630189 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.20 6.86 . . . . . -299 1 173657492 173657494 CCT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 58.89 0.000 7.19 13.13 . . . . . -300 1 17376802 17376803 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04283 12.00 -301 1 17430926 17430926 NA/NA/C/NA NA/NA/CTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 30.00 -302 1 174698334 174698334 T/NA/NA/NA TTTGCTTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.54 9.17 . . . . . -303 1 175504583 175504589 TTTGTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.88 0.000 13.64 11.68 . . . . . -304 1 175922387 175922387 A/NA/NA/NA ATTCACCATTTCTCACAATATTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 8.96 . . . . . -305 1 175956278 175956278 A/NA/NA/NA ATTGGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.22 9.31 . . . . . -306 1 175956279 175956279 A/NA/NA/NA ATGTGGTATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.22 9.31 . . . . . -307 1 17601931 17601931 NA/NA/C/NA NA/NA/AAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 0.00 -308 1 177083556 177083558 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.05 7.91 . . . . . -309 1 17778899 17778899 T/NA/NA/NA TCCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.92 7.33 . . . . . -310 1 17778900 17778900 G/NA/NA/NA GCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.93 7.34 . . . . . -311 1 17792618 17792621 NA/TTTC/NA/TTTC NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 3 30 8.0013e-04 . . -312 1 17796316 17796323 NA/CAAAAAA/NA/CAAAAAAA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 6 15 2.7199e-02 . . -313 1 17796316 17796323 NA/CAAAAAAA/NA/CAAAAAAA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 7 15 2.7199e-02 . . -314 1 177978171 177978171 A/NA/NA/NA ATTGAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.53 9.13 . . . . . -315 1 17820432 17820433 AT/AT/AT/AT A/A/A/A FALSE FALSE TRUE FALSE 60.19 1.528 4.62 19.01 1 33 4.2311e-04 0.00040 9.00 -316 1 178801484 178801484 A/NA/NA/NA ATAGTTATGTGACATAGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 8.94 . . . . . -317 1 179379992 179379992 A/NA/NA/NA AATTTACACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.24 9.51 . . . . . -318 1 18015976 18015976 NA/C/C/NA NA/CCT/CCT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.24026 4.00 -319 1 1804495 1804495 NA/G/NA/NA NA/GT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -320 1 18081080 18081081 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 3 4.2118e-01 . . -321 1 18194209 18194209 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -322 1 1835890 1835893 NA/NA/TATA/NA NA/NA/AT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00210 6.00 -323 1 1841664 1841665 NA/AT/AT/AT NA/A/A/A FALSE TRUE FALSE TRUE . . . . 1 16 2.1346e-02 0.03927 11.00 -324 1 1866058 1866092 TTGTAGGTACACACGTGTGTACGTGGGTGTTAGGC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 56.94 -0.054 6.18 28.25 . . . . . -325 1 18762800 18762801 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 8 1.4170e-01 . . -326 1 18804792 18804792 NA/A/A/A NA/AAC/AAC/AC FALSE FALSE FALSE TRUE . . . . 2 10 8.3333e-02 0.70621 16.00 -327 1 18831510 18831512 TGA/NA/NA/TGA T/NA/NA/T FALSE FALSE FALSE TRUE 60.00 0.000 5.40 4.87 . 7 1.8347e-01 . . -328 1 18881072 18881073 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03699 11.00 -329 1 18983896 18983897 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.04427 11.00 -330 1 19070951 19070951 NA/NA/T/NA NA/NA/TGGATGGATGGATGATGGATGGGTGGATGAGGGATGGATAGAGGATGGATGGATAGAAGGATGGATGGATAGAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00039 13.00 -331 1 19124603 19124603 NA/C/C/C NA/CCCCG/CCCCG/CCCCG FALSE FALSE FALSE TRUE . . . . 4 5 2.9371e-01 0.08148 10.00 -332 1 19256151 19256160 NA/NA/ACTTGAGAGG/NA NA/NA/GGCCAACAGGACT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00005 2.00 -333 1 1928861 1928862 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -334 1 19484946 19484947 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.02878 11.00 -335 1 19628182 19628183 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03406 12.00 -336 1 1963054 1963089 NA/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT NA/G/G/G FALSE FALSE FALSE TRUE . . . . 35 24 3.3714e-03 0.06812 2.00 -337 1 19777212 19777219 AAACTATC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.62 12.71 . . . . . -338 1 19863459 19863459 NA/NA/G/NA NA/NA/ATATATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00132 0.00 -339 1 19873193 19873193 NA/T/NA/NA NA/TA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -340 1 20032285 20032286 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.09528 11.00 -341 1 20068231 20068231 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 13 4.2825e-02 . . -342 1 20259424 20259424 NA/NA/A/NA NA/NA/AATCACCATCACCATTAATTATCACCATCAACATCACCATCGGTGCCATCAACATCATCATCATCACCATCACCATCATCATCATCATTACCATTACCATCACCATCATCATCTTCACCATCACCATCACCATTGCACCATCACCATTATCATCATCTTAATCACTATCAACATCACCATAATAATCACC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 3.00 -343 1 20346159 20346160 NA/GT/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -344 1 20419641 20419644 ATTC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.98 6.59 . . . . . -345 1 2055148 2055148 NA/NA/NA/G NA/NA/NA/GGTC FALSE FALSE FALSE TRUE . . . . . 6 2.0420e-01 . . -346 1 20617658 20617658 NA/A/A/NA NA/AGTGT/AGTGT/NA FALSE FALSE TRUE FALSE . . . . 4 . . 0.03653 8.00 -347 1 20619131 20619133 CGT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.29 7.98 . . . . . -348 1 20708961 20708961 NA/NA/A/A NA/NA/ATGGTGGTGATGGTGGTGATGGTGGTGGTGGGGGGGTAGTGATGGTGGTAATGATTGTGGTGATGGTAGTGGTGATGTTGGTGGTGATGGTGGTGGGGG/ATGG FALSE FALSE TRUE FALSE . . . . . 1 7.8322e-01 0.00007 5.00 -349 1 20780714 20780714 NA/NA/T/NA NA/NA/TGTCTATGTGTCTGTGTGTATCTGTGTGTCTGTGTGCTATGTCTGTTTCTGTGTATATGTCCATGTGTGTCTGTGTGTGTATGTCCATGTGTGTCTGTGTATGTGTCCGTGTGTGTTTCCGTGTCTGTTTCTGTGTGTCCGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00260 6.00 -350 1 20872180 20872180 A/NA/NA/NA ACATCACATTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.51 9.57 . . . . . -351 1 20874279 20874280 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6101e-02 . . -352 1 20934903 20934903 NA/T/T/NA NA/TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGC/TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTAGC/NA FALSE FALSE TRUE FALSE . . . . 35 . . 0.00000 6.00 -353 1 20997998 20997998 NA/A/NA/A NA/AT/NA/AT FALSE TRUE FALSE TRUE . . . . 1 15 3.0395e-02 . . -354 1 21039143 21039146 NA/NA/NA/ATAT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 4 3.5979e-01 . . -355 1 21156502 21156502 G/NA/NA/NA GGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.75 8.94 . . . . . -356 1 2117935 2117935 NA/NA/G/NA NA/NA/GC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.52632 10.00 -357 1 21219986 21219986 G/NA/NA/NA GGGGTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.69 13.23 . . . . . -358 1 21273938 21273939 NA/TA/TA/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.01629 12.00 -359 1 21283110 21283110 NA/NA/C/NA NA/NA/AAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00031 0.00 -360 1 21306249 21306249 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -361 1 21351940 21351941 NA/NA/GA/GA NA/NA/G/G FALSE FALSE FALSE TRUE . . . . . 9 1.1099e-01 0.11538 10.00 -362 1 21367445 21367446 NA/NA/AT/AT NA/NA/A/A FALSE FALSE FALSE TRUE . . . . . 5 2.9247e-01 0.23345 11.00 -363 1 21380959 21380959 NA/T/T/NA NA/TA/TA/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.10502 12.00 -364 1 21381713 21381725 TGATATTTTGCTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.93 9.10 . . . . . -365 1 21409980 21409981 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -366 1 21567673 21567673 G/NA/NA/NA GTCTGTTTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.76 7.54 . . . . . -367 1 21638002 21638002 NA/NA/C/NA NA/NA/AAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -368 1 21744993 21744993 NA/NA/A/A NA/NA/AT/AT FALSE FALSE FALSE TRUE . . . . . 13 4.8364e-02 0.07824 2.00 -369 1 21745022 21745022 NA/A/A/NA NA/ATGTATGTGTATGTGT/GTGT/NA FALSE FALSE TRUE FALSE . . . . 15 . . 0.00312 0.00 -370 1 21745022 21745022 NA/A/A/NA NA/ATGTATATGTATATGT/GTGT/NA FALSE FALSE TRUE FALSE . . . . 15 . . 0.00312 0.00 -371 1 21766605 21766611 NA/TGCAGGC/TGCAGGC/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 6 . . 0.40000 4.00 -372 1 22045057 22045057 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -373 1 22051593 22051593 T/NA/NA/NA TTGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.83 13.08 . . . . . -374 1 22098301 22098301 NA/NA/G/NA NA/NA/GC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 1.00 -375 1 22286329 22286379 NA/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG NA/A/A/A FALSE TRUE FALSE TRUE . . . . 50 57 1.6848e-06 0.32511 1.42 -376 1 22298947 22298947 NA/C/C/NA NA/CAAAAAAAA/CAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 8 . . 0.00000 25.00 -377 1 22350322 22350322 NA/NA/A/NA NA/NA/AAC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 24.00 -378 1 22411737 22411737 NA/A/A/NA NA/AAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00001 18.00 -379 1 22411737 22411737 NA/A/A/NA NA/AAAAAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 6 . . 0.00001 18.00 -380 1 22411737 22411737 NA/A/A/NA NA/AAAAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 5 . . 0.00001 18.00 -381 1 22415050 22415050 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 9.09 . . . . . -382 1 22415051 22415051 G/NA/NA/NA GGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 9.09 . . . . . -383 1 22436691 22436692 NA/NA/TA/TA NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 7 1.6452e-01 0.48571 12.00 -384 1 22657975 22657976 NA/CA/NA/CA NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 15 3.1352e-02 . . -385 1 22673892 22673895 NA/AAAG/AAAG/AAAG NA/A/A/A FALSE FALSE FALSE TRUE . . . . 3 14 3.9130e-02 1.00000 15.00 -386 1 2274296 2274297 NA/AT/NA/AT NA/A/NA/A FALSE FALSE FALSE TRUE . . . . 1 31 7.5783e-04 . . -387 1 22794581 22794582 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -388 1 22800392 22800392 T/NA/NA/NA TCTTTTCATATTCTAAATAATACTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.94 8.95 . . . . . -389 1 22904548 22904548 NA/NA/G/NA NA/NA/GCATGTGTGCATGAGTATGTATGCATGTGTGTGCATGTAGCGTCAGTGTATGCATGTGTGCGTGAGTGTATGCATGTGTGCATGTGATGCGTATGTATGCATGCGTGTGCATGTGTGTGACTATGTATGCATGTGTGTATGTATGCGTGTGTGTGCATGTGTGCGTGAGTATGTGCATTGAGTGCATGCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00012 4.00 -390 1 22905084 22905084 NA/NA/G/NA NA/NA/GTGTGTGCATGTGTGCATGAGTGTATGTGCAATGTGCGTGTGCATGTGTGTGAGTGTATGCATGTGTGCGTGCACATGTGTGCGAGTGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.05690 1.00 -391 1 22944533 22944533 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -392 1 22967697 22967699 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.60 8.84 . . . . . -393 1 23004825 23004829 NA/NA/NA/ACGTG NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 11 7.3359e-02 . . -394 1 2302665 2302665 NA/C/C/C NA/CACAACCACA/CACAACCACA/CACAACCACA FALSE FALSE FALSE TRUE . . . . 9 11 7.9421e-02 1.00000 6.00 -395 1 23130236 23130238 NA/GTA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 2 . . . . -396 1 23161118 23161118 NA/C/C/NA NA/CA/CA/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.05183 12.00 -397 1 23275378 23275378 T/NA/NA/NA TAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 6.38 . . . . . -398 1 23275380 23275380 C/NA/NA/NA CCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 6.38 . . . . . -399 1 2332705 2332706 NA/NA/AC/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.27126 5.00 -400 1 23381505 23381505 G/NA/NA/NA GAATATTTTTTATTATTTATTTATTATATTTAACTTGACTTATAAGAAGATAAACTTGGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 . 11.74 9.28 . . . . . -401 1 23443935 23443936 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04685 11.00 -402 1 23524562 23524563 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -403 1 23562170 23562170 G/NA/NA/NA GGTTTCCTTAGCAATTCTATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.50 9.21 . . . . . -404 1 236111 236112 NA/CT/CT/CT NA/C/C/C FALSE TRUE FALSE TRUE . . . . 1 21 6.8801e-03 0.01296 4.00 -405 1 23662609 23662609 NA/C/C/NA NA/CA/CAAAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 28.00 -406 1 23718938 23718942 NA/NA/A/AATAC NA/NA/ATACTCCATACATC/A FALSE FALSE TRUE FALSE . . . . . 0 8.8112e-01 0.00976 2.00 -407 1 237528 237529 NA/CA/NA/C NA/CAAAAA/NA/CAAAA FALSE FALSE FALSE TRUE . . . . 4 18 1.5361e-02 . . -408 1 237528 237529 NA/CA/NA/C NA/C/NA/CAAAA FALSE FALSE FALSE TRUE . . . . 1 18 1.5361e-02 . . -409 1 23821722 23821722 NA/NA/A/NA NA/NA/AGAGTAACAGGCTTAGGACAATTACGATGTGAGGAGTAATAGGCCTAGGACAATTACGATGTGAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -410 1 23922256 23922260 GCATT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.90 7.63 . . . . . -411 1 23952454 23952454 NA/NA/G/NA NA/NA/GATAATGATAGGGATGATGGTGATGGTGATGATGATGGTGATGATGGGGATGATGGTGATGGTGATGATGGTGATGTTGATGAATGGTGGTGATGGTGGCAATGTTGGTGATGATGGTAATGATAATGGTGGTGGAGGTGATGATGATGATGATAAGGATGATAATGATGGTGGAGGTGATGATCATGGTAAAGGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00214 2.00 -412 1 23952478 23952478 NA/NA/G/NA NA/NA/GCTGATGGTATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02556 2.00 -413 1 24030192 24030199 NA/TATATTAC/TATATTAC/NA NA/T/T/NA FALSE TRUE TRUE FALSE . . . . 7 . . 0.08333 3.00 -414 1 24072002 24072002 NA/A/NA/A NA/AT/NA/AT FALSE FALSE FALSE TRUE . . . . 1 13 4.6702e-02 . . -415 1 24173832 24173832 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -416 1 24226300 24226303 NA/CAGA/C/C NA/CAAGA/CAGAAAGAAAGAAAGAAAAGAAAAAAAAGAAAGAAAAGAAAGAAAGAAAGGAAAGAAGGAAAGAAAGAAAGAA/CA FALSE FALSE TRUE FALSE . . . . 1 0 8.1818e-01 0.00014 7.00 -417 1 24226300 24226303 NA/CAGA/C/C NA/C/CAGAAAGAAAGAAAGAAAAGAAAAAAAAGAAAGAAAAGAAAGAAAGAAAGGAAAGAAGGAAAGAAAGAAAGAA/CA FALSE FALSE TRUE FALSE . . . . 3 0 8.1818e-01 0.00014 7.00 -418 1 24290087 24290087 NA/C/C/NA NA/CAT/CAT/NA FALSE TRUE FALSE FALSE . . . . 2 . . 1.00000 6.00 -419 1 24357747 24357748 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.6374e-01 . . -420 1 24481706 24481708 ATG/NA/ATG/NA A/NA/A/NA FALSE FALSE TRUE FALSE 60.00 0.000 7.17 4.60 . . . 0.01868 7.00 -421 1 24490069 24490072 NA/NA/CTTT/CTTT NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 13 4.8515e-02 0.02017 6.00 -422 1 24617119 24617119 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -423 1 24671680 24671681 NA/NA/NA/GC NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 5 2.8571e-01 . . -424 1 25075718 25075718 NA/T/T/T NA/TA/TA/TA FALSE FALSE FALSE TRUE . . . . 1 14 3.5410e-02 0.01264 15.00 -425 1 25091149 25091149 NA/G/NA/NA NA/GA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -426 1 25129202 25129203 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 14 3.8037e-02 . . -427 1 25322776 25322777 NA/NA/CA/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -428 1 253243 253245 NA/NA/ACT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01367 4.00 -429 1 2540473 2540477 NA/TACAC/NA/TACAC NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 4 3 4.0806e-01 . . -430 1 25523209 25523209 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -431 1 25613276 25613276 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -432 1 2584644 2584646 ACC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 35.04 -2.399 147.53 34.17 . . . . . -433 1 2589688 2589688 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 13 4.7679e-02 . . -434 1 2597367 2597368 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.9804e-01 . . -435 1 26149013 26149018 NA/NA/NA/CTTTTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 15 2.8215e-02 . . -436 1 2619639 2619640 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 14 3.7486e-02 . . -437 1 26204890 26204894 NA/NA/TATAA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.13009 9.00 -438 1 26235126 26235135 NA/NA/TATTATTATT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 16.00 -439 1 2627109 2627109 C/NA/NA/NA CCTG/NA/NA/NA TRUE FALSE FALSE FALSE 21.73 -1.581 13.20 7.26 . . . . . -440 1 26555930 26555930 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 16 2.1834e-02 . . -441 1 26567735 26567735 NA/NA/A/NA NA/NA/ATTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 26.00 -442 1 26583087 26583087 NA/NA/T/T NA/NA/TTTTC/TTTTC FALSE FALSE TRUE TRUE . . . . . 12 5.2632e-02 0.04801 4.00 -443 1 26711805 26711806 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6023e-02 . . -444 1 26762892 26762896 TTTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.211 18.32 11.04 . . . . . -445 1 26765217 26765217 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 9 1.0714e-01 . . -446 1 26838847 26838847 NA/NA/T/NA NA/NA/TACACACACAAACACACACACACACACACACACACAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 3.00 -447 1 2693465 2693466 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 20 9.6796e-03 . . -448 1 27172802 27172802 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 6 2.4074e-01 . . -449 1 27222134 27222135 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 13 4.0642e-02 0.01346 12.00 -450 1 27224144 27224149 AGGGTG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 24.01 7.83 . . . . . -451 1 27387962 27387963 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 18 1.3426e-02 0.00194 23.00 -452 1 27402731 27402731 NA/NA/C/NA NA/NA/GAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.06179 0.00 -453 1 27433686 27433686 NA/NA/C/NA NA/NA/CACACACACACACACCCACACACACCCATCTCCACACATACACACACAGCCCCTCCACACACAAACCCATCTCCAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00056 9.00 -454 1 27433722 27433723 NA/NA/AA/NA NA/NA/CCACACACCCACCCAGCCCCTCCACACACACACCCACACCCACACACCCAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00004 0.00 -455 1 27471564 27471564 NA/NA/G/G NA/NA/GA/GA FALSE FALSE FALSE TRUE . . . . . 17 1.8258e-02 0.00008 18.00 -456 1 27474486 27474487 NA/NA/CA/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01155 11.00 -457 1 27580005 27580006 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 7 1.7787e-01 . . -458 1 27612958 27612959 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6233e-02 . . -459 1 27647392 27647393 NA/NA/CT/CT NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 8 1.5826e-01 0.10122 12.00 -460 1 27699264 27699264 NA/NA/A/NA NA/NA/TTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00014 0.00 -461 1 27966096 27966098 NA/NA/NA/CTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.8176e-02 . . -462 1 28002090 28002091 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00930 11.00 -463 1 28243107 28243107 T/NA/T/NA TTGTGTGTGTGTG/NA/TTGTGTGTGTGTG/NA FALSE FALSE TRUE FALSE 57.63 -0.669 1.80 4.57 . . . 0.00004 25.00 -464 1 28257344 28257344 NA/NA/NA/T NA/NA/NA/TTACA FALSE FALSE FALSE TRUE . . . . . 13 4.4118e-02 . . -465 1 28333848 28333849 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 20 8.0769e-03 . . -466 1 28534251 28534254 NA/NA/NA/CCAA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 19 1.1811e-02 . . -467 1 28582245 28582245 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.294 12.04 6.51 . . . . . -468 1 28595993 28595994 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.3278e-02 . . -469 1 28639103 28639105 AAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.35 -6.777 19.85 7.60 . . . . . -470 1 28684150 28684346 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAAGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATCTTGCCACTGCACTCCAGCCGGGGCCACAGAGCGAGACTCCGTCTCCAAAAAAAATAAAAAATAAAAATAAATAAAAATAAAAATACAAAAAATTAGCCGGGCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 58.48 -2.472 8.25 7.54 . . . . . -471 1 28884574 28884575 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 13 4.9439e-02 . . -472 1 28924881 28924884 CTTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.09 8.02 . . . . . -473 1 28962326 28962327 NA/NA/NA/GT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 14 3.2898e-02 . . -474 1 28998896 28998897 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.9192e-01 . . -475 1 29169478 29169478 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 6 2.4074e-01 . . -476 1 29259017 29259018 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 10 8.7702e-02 . . -477 1 2937914 2937916 NA/GTC/NA/GTC NA/G/NA/G FALSE TRUE FALSE TRUE . . . . 2 17 1.6968e-02 . . -478 1 2942459 2942459 NA/NA/G/NA NA/NA/GATGACAGTGATGGTGATGATGGTAATGACAATGATGGTGATGATGATGGTGATGATGGTGATGGTGATGATGATGGTGATGATGGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00041 2.00 -479 1 2942467 2942467 NA/NA/T/NA NA/NA/TGATGGTGATGATGATGGTAATGACATGGTGGTGTGATCATGATGATGGTGAGGATGGTGGTGGTGATGATGGTAGCTGGTGACGATAATGATGGTGGTGATGATGGTGATGATGACAATGATGGTGATCATGATGGTGATGATGATGGTGATGGC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00013 1.00 -480 1 2961928 2961928 G/NA/NA/NA GGATCAAGGAGTCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 12.82 . . . . . -481 1 2985542 2985543 NA/AG/AG/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 1.00000 11.00 -482 1 30651234 30651234 T/NA/NA/NA TTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 6.32 . . . . . -483 1 3098037 3098052 NA/NA/CGCAGTCTTACACACA/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01121 3.00 -484 1 31411751 31411751 T/NA/NA/NA TAGAC/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 . 13.37 7.88 . . . . . -485 1 3177306 3177306 NA/NA/A/NA NA/NA/ATGATGTTGGTGATGGTGGTGATGATGATGGCATGATGGCAGTGATTCAAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 3.00 -486 1 3187224 3187225 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -487 1 3187225 3187228 NA/NA/AGGA/NA NA/NA/GG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00005 2.00 -488 1 3187227 3187228 NA/GA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -489 1 3236878 3236880 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 21.28 6.59 . . . . . -490 1 32917655 32917659 GTATT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.87 0.000 18.74 7.35 . . . . . -491 1 3398879 3398879 NA/G/G/NA NA/GGGGGGGCGGGTAGCC/GGGGGGGCGGGTAGCC/NA FALSE TRUE FALSE FALSE . . . . 15 . . 1.00000 7.00 -492 1 3403148 3403148 A/NA/NA/NA AGAGTTAACTACAAACAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.31 6.33 . . . . . -493 1 3500398 3500434 NA/NA/GCAGCCACCAGACAACCCGCAGCCACCAGACAACGCG/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.12253 2.00 -494 1 3500449 3500449 NA/C/C/NA NA/CGCACAGCCACCAGACAAT/CGCACAGCCACCAGACAAT/NA FALSE FALSE TRUE FALSE . . . . 18 . . 0.00000 1.00 -495 1 35008216 35008216 A/NA/NA/NA ACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.75 12.06 . . . . . -496 1 3504600 3504623 NA/NA/CCAGGAGGGGGCAGGACAGGGCAG/NA NA/NA/ATAGGAGGAGATAGGAGGGGACAGGAGTGGACAGAAGGAGACAGGAGGGGACAGGAGTGGACAGGAGACAGGAGGGGACAGGAATGGCCAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00699 0.00 -497 1 35731970 35731973 AAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.07 11.068 27.24 6.94 . . . . . -498 1 36026087 36026092 CCTGCT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.75 8.63 . . . . . -499 1 3610560 3610560 NA/NA/C/C NA/NA/CT/CT FALSE FALSE FALSE TRUE . . . . . 4 3.3766e-01 0.50000 4.00 -500 1 36624636 36624640 GTTAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.95 0.324 12.85 14.19 . . . . . -501 1 37262884 37262886 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.37 12.36 . . . . . -502 1 3738791 3738810 NA/NA/GACTGACAGACAGACAGAGG/NA NA/NA/CC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 6.00 -503 1 3785163 3785163 NA/NA/A/NA NA/NA/ACCACACCATACCAGACCACACCACACCAGGCCACACCACACCAAGCCACAACCACGCCACACCACACCAGG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -504 1 37917967 37917967 G/NA/NA/NA GAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 34.93 7.49 . . . . . -505 1 37917968 37917968 T/NA/NA/NA TTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 34.94 7.24 . . . . . -506 1 3801133 3801134 NA/NA/AT/AT NA/NA/A/A FALSE FALSE TRUE TRUE . . . . . 14 3.2147e-02 0.02997 11.00 -507 1 3816054 3816074 NA/CCAGACACTGGCACCCCCCTT/CCAGACACTGGCACCCCCCTT/CCAGACACTGGCACCCCCCTT NA/C/C/C FALSE FALSE FALSE TRUE . . . . 20 30 9.0133e-04 0.02310 2.00 -508 1 3825025 3825025 NA/NA/T/NA NA/NA/TCTCACA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00006 21.00 -509 1 39487 39487 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 24 3.7652e-03 . . -510 1 39790775 39790775 T/NA/NA/NA TAAGTTTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.81 19.73 . . . . . -511 1 40279122 40279124 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.31 0.271 9.93 6.93 . . . . . -512 1 40803798 40803798 A/NA/NA/NA AAAATGCATGTACCACAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 19.26 6.32 . . . . . -513 1 41069654 41069656 TGA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.12 12.95 . . . . . -514 1 41091997 41091999 TAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.07 15.18 . . . . . -515 1 4110792 4110793 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -516 1 4127223 4127223 NA/NA/NA/T NA/NA/NA/TCATG FALSE FALSE FALSE TRUE . . . . . 4 3.5478e-01 . . -517 1 41599553 41599553 T/NA/NA/NA TAGATTTTCTA/NA/NA/NA TRUE FALSE FALSE FALSE 59.67 -4.282 9.91 9.41 . . . . . -518 1 4363250 4363294 NA/NA/CTCCACCCGACCCCACCCCACCCCACCCCACCCCACCCCACCCCA/NA NA/NA/ATAAATTCCTTTCGAGAGCATTCAATTTAGATGCATTCCATTCGAGTCCATTCCATTCTATTCCATTCCATTTCATTCCATTCAATTCCATTCATATCCACTCGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -519 1 43801445 43801445 G/NA/NA/NA GCATATATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.11 6.37 . . . . . -520 1 44170440 44170442 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 3.841 7.46 6.30 . . . . . -521 1 44643868 44643868 A/NA/NA/NA AATTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.05 . . . . . -522 1 44925096 44925096 C/NA/NA/NA CTTATTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.73 6.59 . . . . . -523 1 45456018 45456018 T/NA/NA/NA TAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.56 9.36 . . . . . -524 1 4603741 4603741 NA/NA/C/NA NA/NA/CTATCTATCTATCTATCTATCTCTCTATCTATCTATCTATCTTATCTATTTATCTATCTATCTATCATCTACCTATCTCTCTGTCATCTATCTATCTCTCTGCCTTTGTGTCTATCTACCTATCTCTATCATCTATCTAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -525 1 4820251 4820253 CTG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.37 -0.494 5.58 6.50 . . . . . -526 1 4827659 4827697 NA/NA/TTATCATCATCACCATCTTTATCATTACCATCATCACCA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00230 2.00 -527 1 48649644 48649644 T/NA/NA/NA TAAAGCATAGCAAGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.85 15.84 . . . . . -528 1 49106010 49106010 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.57 . . . . . -529 1 4931550 4931552 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 -0.201 22.99 6.94 . . . . . -530 1 4942374 4942375 NA/AT/AT/NA NA/A/A/NA FALSE TRUE TRUE FALSE . . . . 1 . . 0.02211 12.00 -531 1 4948380 4948380 NA/NA/C/NA NA/NA/CAAAAAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 18.00 -532 1 49555455 49555457 GAC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.88 6.54 . . . . . -533 1 49862038 49862040 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.21 8.15 . . . . . -534 1 4999496 4999496 NA/NA/G/NA NA/NA/GTCTCTCCATATGACGTCAGTGTCCTCCATATGACATCAATATCCTCCATATGATGTCAATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 1.00 -535 1 49997601 49997601 C/NA/NA/NA CAACAGTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.60 8.94 . . . . . -536 1 50089515 50089515 A/NA/NA/NA ATTTAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 8.87 . . . . . -537 1 50241552 50241552 T/NA/NA/NA TTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 11.88 . . . . . -538 1 50289048 50289048 T/NA/NA/NA TAAATTGATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.44 16.95 . . . . . -539 1 50289049 50289049 C/NA/NA/NA CATACGGTTGATTTGTATGTGTATAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.39 16.95 . . . . . -540 1 5084764 5084764 NA/NA/A/NA NA/NA/AAAATAAATAAATAAAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00734 12.00 -541 1 51049318 51049318 C/NA/NA/NA CAGTGAAACA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.13 . . . . . -542 1 51067364 51067366 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.02 3.388 16.53 11.51 . . . . . -543 1 51146696 51146699 GAAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 12.26 . . . . . -544 1 51177132 51177132 T/NA/NA/NA TAGATCGGAAGAGCGTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.68 7.31 . . . . . -545 1 51640089 51640089 G/NA/NA/NA GATGGTATTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.23 6.43 . . . . . -546 1 51690830 51690830 C/NA/NA/NA CAAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.36 9.27 . . . . . -547 1 5180539 5180539 NA/NA/C/NA NA/NA/AAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -548 1 51844686 51844686 C/NA/NA/NA CTTTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.48 9.18 . . . . . -549 1 51844688 51844688 T/NA/NA/NA TTTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.18 . . . . . -550 1 52434901 52434901 C/NA/NA/NA CAAGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.60 9.63 . . . . . -551 1 52468797 52468799 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.95 6.95 . . . . . -552 1 52535438 52535438 T/NA/NA/NA TCATATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.49 13.23 . . . . . -553 1 5325296 5325297 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 9 1.1565e-01 . . -554 1 53485886 53485886 G/NA/NA/NA GTTGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.66 8.94 . . . . . -555 1 540710 540712 CGA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 51.65 -1.451 13.57 13.14 . . . . . -556 1 547113 547115 NA/NA/NA/GGT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 22 5.2405e-03 . . -557 1 547217 547219 NA/NA/NA/GGT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 13 4.8200e-02 . . -558 1 5498907 5498910 NA/NA/NA/CTTA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.5850e-02 . . -559 1 55983974 55983984 ATCCATCCATC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.62 0.000 11.36 8.91 . . . . . -560 1 5609675 5609675 C/NA/NA/NA CCCACCG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.55 9.22 . . . . . -561 1 56362200 56362203 AGCC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.84 19.33 . . . . . -562 1 56513091 56513091 A/NA/NA/NA AACTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.37 . . . . . -563 1 56513093 56513097 CATCA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.94 9.24 . . . . . -564 1 5664508 5664508 NA/NA/C/NA NA/NA/CTCTCTCTCTCTCATCTCTGTCTTTCTCTCTCTCTCTCATCTCTCTCCCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00032 14.00 -565 1 57581791 57581791 G/NA/NA/NA GCTTCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 6.32 . . . . . -566 1 5810611 5810615 TTGTC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.12 7.536 15.85 13.42 . . . . . -567 1 58262211 58262214 GATA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.000 19.27 10.63 . . . . . -568 1 5855966 5855983 NA/ACCAGTACTCAGTCACCG/ACCAGTACTCAGTCACCG/ACCAGTACTCAGTCACCG NA/A/A/A FALSE FALSE FALSE TRUE . . . . 17 14 3.5344e-02 0.00000 1.00 -569 1 5872338 5872339 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 9 1.2468e-01 . . -570 1 58794335 58794335 T/NA/NA/NA TAACGCTGTGGTTGTAGTATTTCCAAGC/NA/NA/NA TRUE FALSE FALSE FALSE 59.83 0.000 23.61 7.89 . . . . . -571 1 5881482 5881482 NA/NA/G/NA NA/NA/GGAAGGAAGGAAAGAGAGAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 10.00 -572 1 58938598 58938598 G/NA/NA/NA GAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.60 6.82 . . . . . -573 1 59008389 59008389 G/NA/NA/NA GTATTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.18 4.398 9.96 9.46 . . . . . -574 1 59726039 59726040 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.61 6.49 . . . . . -575 1 59726041 59726048 TGTGTGTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.17 6.49 . . . . . -576 1 5973211 5973212 NA/CA/NA/CA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 18 1.4590e-02 . . -577 1 5986573 5986573 C/NA/NA/NA CA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 27.39 8.05 . . . . . -578 1 5992132 5992133 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 10 9.3583e-02 . . -579 1 60264195 60264195 T/NA/NA/NA TGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.56 9.05 . . . . . -580 1 6065211 6065212 NA/NA/AC/NA NA/NA/TT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.51471 1.00 -581 1 6065447 6065447 NA/NA/NA/G NA/NA/NA/GT FALSE FALSE FALSE TRUE . . . . . 7 1.9231e-01 . . -582 1 6065495 6065495 NA/NA/G/NA NA/NA/GAGCTGAGTGGGGTGACGTGGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00023 3.00 -583 1 6065981 6065982 NA/NA/NA/TC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 10 9.4721e-02 . . -584 1 6066218 6066219 NA/NA/TC/TC NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 5 2.5926e-01 0.53770 6.00 -585 1 61356823 61356825 GGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.09 6.71 . . . . . -586 1 61631966 61631966 A/NA/NA/NA AAGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.58 12.82 . . . . . -587 1 61631967 61631967 T/NA/NA/NA TGTCTAAGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.58 12.82 . . . . . -588 1 63013003 63013003 A/NA/NA/NA AGAGTACAGCAAAGTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.15 9.11 . . . . . -589 1 63117847 63117850 TCCC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.34 12.35 . . . . . -590 1 6332302 6332306 GATGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 23.18 7.59 . . . . . -591 1 6366267 6366267 NA/NA/A/A NA/NA/AGAGGGG/AGAGGGG FALSE FALSE FALSE TRUE . . . . . 4 3.2353e-01 0.65289 5.00 -592 1 63986883 63986883 A/NA/NA/NA ATTTGTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.10 9.69 . . . . . -593 1 6417930 6417930 NA/C/NA/C NA/CTT/NA/CTT FALSE FALSE FALSE TRUE . . . . 2 14 3.9629e-02 . . -594 1 65018790 65018790 G/NA/NA/NA GTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.25 15.79 . . . . . -595 1 65190377 65190377 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.65 8.94 . . . . . -596 1 65190379 65190379 T/NA/NA/NA TGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.66 8.94 . . . . . -597 1 6530965 6530965 NA/C/C/NA NA/CG/CG/NA FALSE TRUE FALSE FALSE . . . . 1 . . 1.00000 4.00 -598 1 6541922 6541923 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -599 1 65523704 65523704 T/NA/NA/NA TTTACATGAAAATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.63 8.90 . . . . . -600 1 6582943 6582943 NA/C/C/NA NA/CAA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 0.00 -601 1 6582943 6582943 NA/C/C/NA NA/CAAA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 0.00 -602 1 6582943 6582943 NA/C/C/NA NA/CA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 0.00 -603 1 6583221 6583221 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 24 3.7764e-03 . . -604 1 66451871 66451878 CACAATGT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.74 9.33 . . . . . -605 1 6660077 6660079 AAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.46 6.97 . . . . . -606 1 6666725 6666726 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 5 2.8571e-01 . . -607 1 6724301 6724302 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 18 1.4821e-02 . . -608 1 6734787 6734787 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -609 1 67359685 67359685 A/NA/NA/NA AGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 12.82 . . . . . -610 1 67576182 67576182 A/NA/NA/NA AACAGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 12.70 . . . . . -611 1 6777615 6777615 A/NA/NA/NA ATTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.96 9.46 . . . . . -612 1 68212752 68212752 A/NA/NA/NA ATAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 8.77 . . . . . -613 1 68393888 68393888 C/NA/NA/NA CATTAAAAAAAGATATGCAGCCAGGCGCAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.59 6.55 . . . . . -614 1 6894212 6894212 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 6 2.2973e-01 . . -615 1 69009958 69009958 T/NA/NA/NA TGG/NA/NA/NA TRUE FALSE FALSE FALSE 59.70 -4.827 7.53 10.45 . . . . . -616 1 69192187 69192187 T/NA/NA/NA TGATTTAAGTAAAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.85 9.69 . . . . . -617 1 693620 693621 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 49.88 -2.429 10.18 6.56 . . . . . -618 1 69725408 69725408 A/NA/NA/NA AAAAATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.37 8.91 . . . . . -619 1 69725409 69725409 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 8.91 . . . . . -620 1 6997794 6997796 NA/NA/AGT/NA NA/NA/CATCATTCTCACTACCAC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00879 0.00 -621 1 7000990 7000991 NA/NA/AA/NA NA/NA/GGGGGGTCCTCAGAGGGAGAGGGATCCTCCCGGGGAAGGGGGATCCTCACGGGGAAGGGCATCCTCAGGGGGAAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -622 1 70015621 70015621 A/NA/NA/NA ACATAAATTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.99 12.02 . . . . . -623 1 70040383 70040383 C/NA/NA/NA CTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 22.88 16.48 . . . . . -624 1 70040384 70040384 A/NA/NA/NA ATCTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 22.88 16.47 . . . . . -625 1 70070001 70070001 T/NA/NA/NA TAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.95 12.65 . . . . . -626 1 7007607 7007608 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -627 1 7044150 7044150 NA/NA/G/NA NA/NA/ATGAATGGATGGTTGGGTGGATGGATGGGTTGGATGAGTGAACCGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00522 0.00 -628 1 70766861 70766863 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.61 7.90 . . . . . -629 1 71104257 71104257 C/NA/NA/NA CTAGCTGTACATTAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.64 6.38 . . . . . -630 1 71787025 71787025 A/NA/NA/NA AGTGCTTGATAT/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.282 10.27 9.02 . . . . . -631 1 7216335 7216336 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -632 1 7226868 7226868 NA/G/NA/NA NA/GT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -633 1 72340027 72340027 A/NA/NA/NA AATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.76 8.98 . . . . . -634 1 72602225 72602225 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.37 . . . . . -635 1 72602226 72602226 A/NA/NA/NA AACAATAATAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.37 . . . . . -636 1 72657998 72657998 G/NA/NA/NA GATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.65 13.39 . . . . . -637 1 72799605 72799605 A/NA/NA/NA AATAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.42 9.90 . . . . . -638 1 72930915 72930915 A/NA/NA/NA AGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.52 . . . . . -639 1 7370802 7370802 NA/NA/C/C NA/NA/TT/CTTTTT FALSE FALSE FALSE TRUE . . . . . 4 3.4737e-01 1.00000 0.00 -640 1 74138051 74138051 T/NA/NA/NA TATATATATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.68 13.08 . . . . . -641 1 74538174 74538176 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.31 4.939 5.18 7.18 . . . . . -642 1 74663493 74663493 G/NA/NA/NA GTTTTTTTGGGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.09 6.65 . . . . . -643 1 7489683 7489683 NA/NA/G/NA NA/NA/GTGATAATGATGATGATGGTGATGACAGTGCTGATAATAGATCATAATGGTGATGATGATGATGGTGATTATTGTAATAGTGATGACAGTGATGATGATAATGATGGTGATAAGAGTGGATAATGATAATAACACTAATGGTGATGATGATAATGATGGTGGTATGATGATGTGGATGGTAATGGTGATGATAACAGTGGATAATGATGGCAATGCAAGTGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -644 1 74987200 74987202 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.30 -0.322 8.20 6.50 . . . . . -645 1 7506241 7506242 NA/GA/NA/GA NA/G/NA/G FALSE FALSE FALSE TRUE . . . . 1 13 4.3944e-02 . . -646 1 75275380 75275380 T/NA/NA/NA TATAATTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 9.26 . . . . . -647 1 7662140 7662140 NA/NA/NA/T NA/NA/NA/TTTCC FALSE FALSE FALSE TRUE . . . . . 5 2.6815e-01 . . -648 1 76986983 76986985 TAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.17 4.398 10.49 7.19 . . . . . -649 1 77032198 77032206 CTCTTTCTT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.62 13.56 . . . . . -650 1 77354419 77354419 A/NA/NA/NA ATAGGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.93 9.57 . . . . . -651 1 77367889 77367889 T/NA/NA/NA TATCATGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 9.17 . . . . . -652 1 7762392 7762396 AAAAC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.34 6.73 . . . . . -653 1 77712396 77712396 T/NA/NA/NA TCCC/NA/NA/NA TRUE FALSE FALSE FALSE 59.47 -6.890 9.30 13.86 . . . . . -654 1 7825019 7825020 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -655 1 78854924 78854924 A/NA/NA/NA AATGATGGT/NA/NA/NA TRUE FALSE FALSE FALSE 54.76 -2.406 4.52 6.92 . . . . . -656 1 79475391 79475391 T/NA/NA/NA TTTG/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 . 7.29 7.80 . . . . . -657 1 79615102 79615102 T/NA/NA/NA TGATTGTCCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.37 8.94 . . . . . -658 1 79879535 79879535 A/NA/NA/NA AGCCATGGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.87 9.75 . . . . . -659 1 80078641 80078641 T/NA/NA/NA TTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 13.38 . . . . . -660 1 80209962 80209962 T/NA/NA/NA TAACA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.49 16.40 . . . . . -661 1 80229884 80229886 TCA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.04 8.47 . . . . . -662 1 8041720 8041721 NA/GT/NA/G NA/G/NA/GTT FALSE FALSE FALSE TRUE . . . . 1 13 4.8663e-02 . . -663 1 8041720 8041721 NA/GT/NA/G NA/GTTT/NA/GTT FALSE FALSE FALSE TRUE . . . . 2 13 4.8663e-02 . . -664 1 80557556 80557556 A/NA/NA/NA ATATAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.87 8.91 . . . . . -665 1 8087009 8087009 NA/NA/A/NA NA/NA/AGGGACAGTGAGAGTGAGGGACAGTGTAGGACAGTGAGGGACAGTGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 -666 1 8117228 8117229 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02760 11.00 -667 1 81654021 81654022 CA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.70 26.96 . . . . . -668 1 81685072 81685072 T/NA/NA/NA TTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 8.87 . . . . . -669 1 81927897 81927897 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.37 10.45 . . . . . -670 1 81927899 81927899 A/NA/NA/NA ATTCTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.36 10.45 . . . . . -671 1 820722 820724 NA/NA/NA/GCT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 14 3.4521e-02 . . -672 1 820723 820733 NA/NA/CTATCCTTAAC/NA NA/NA/AACCTTATCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00362 2.00 -673 1 820733 820733 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 12 5.2656e-02 . . -674 1 820749 820749 NA/NA/C/NA NA/NA/CT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00903 6.00 -675 1 8212709 8212709 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -676 1 8217903 8217940 NA/NA/TGGAAGAGGAGGAGGAAGAAGAAGGAGAAGAAGGAAGA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01367 2.00 -677 1 825392 825449 NA/NA/CTATTTTTTCTTTTGTTGGGGGGGTGGGGAGGTGGATGGAGTCTCACTCTGTCACCCG/NA NA/NA/TCTTTTTTTTTTTGCTGGGGGTGGGGTGTGGTGGATGGAATCTTGCTCTGATGCCCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00408 6.00 -678 1 82571241 82571241 G/NA/NA/NA GGGAGAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.36 12.71 . . . . . -679 1 82571243 82571243 A/NA/NA/NA ATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.36 12.71 . . . . . -680 1 8276437 8276438 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 13 4.1046e-02 0.18148 11.00 -681 1 82979355 82979355 T/NA/NA/NA TGACATAAACAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.46 12.87 . . . . . -682 1 83044829 83044834 ATGGGG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.82 9.83 . . . . . -683 1 8321412 8321442 NA/TCTTTCTTTCCTTCCTTCCTTCCTTCCTTCC/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 30 . . . . -684 1 83215295 83215295 A/NA/NA/NA ATC/NA/NA/NA TRUE FALSE FALSE FALSE 59.75 0.000 12.38 8.81 . . . . . -685 1 83215297 83215297 A/NA/NA/NA AAAGAATAGTAT/NA/NA/NA TRUE FALSE FALSE FALSE 59.74 0.000 12.38 8.81 . . . . . -686 1 8328298 8328300 NA/CT/NA/CTT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 11 7.2188e-02 . . -687 1 83332 83332 NA/NA/G/G NA/NA/GA/GA FALSE FALSE TRUE FALSE . . . . . 4 3.5296e-01 0.11415 3.00 -688 1 83571902 83571905 TTAA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.61 7.61 . . . . . -689 1 83903033 83903034 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 54.28 -2.659 12.94 7.14 . . . . . -690 1 8427001 8427002 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 9 1.1103e-01 . . -691 1 85297559 85297561 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.91 7.08 . . . . . -692 1 85992513 85992513 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 24.04 8.07 . . . . . -693 1 86005852 86005852 G/NA/NA/NA GTGGGCTCAATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.77 9.09 . . . . . -694 1 86005854 86005854 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 9.09 . . . . . -695 1 86190136 86190142 AGTAGCT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.39 8.50 . . . . . -696 1 86229006 86229011 CACAAG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.60 10.34 . . . . . -697 1 86247418 86247418 A/NA/NA/NA AGATTATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 12.22 . . . . . -698 1 8624885 8624885 A/A/A/NA ATATGTGTGTGTGTG/ATATGTGTGTGTGTG/ATATGTGTGTGTGTG/NA FALSE FALSE TRUE FALSE 54.85 . 1.55 4.44 14 . . 0.00940 8.00 -699 1 86285375 86285375 G/NA/NA/NA GATTCATA/NA/NA/NA TRUE FALSE FALSE FALSE 59.63 0.000 7.55 12.60 . . . . . -700 1 86383049 86383049 C/NA/NA/NA CAGTATTGGTCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.26 9.62 . . . . . -701 1 8655217 8655218 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -702 1 8661076 8661076 NA/C/NA/C NA/CTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 2 13 4.5516e-02 . . -703 1 8661076 8661076 NA/C/NA/C NA/CTTTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 4 13 4.5516e-02 . . -704 1 8661076 8661076 NA/C/NA/C NA/CTTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 3 13 4.5516e-02 . . -705 1 8696001 8696011 NA/NA/TTTATTTTATC/TTTATTTTATC NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 15 2.9557e-02 0.21037 6.00 -706 1 87347091 87347091 T/NA/NA/NA TTTTATTAAGTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.37 9.09 . . . . . -707 1 8738547 8738548 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -708 1 87663930 87663932 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.71 6.75 . . . . . -709 1 87863468 87863468 A/NA/NA/NA ATCCCTGTCCCACACCAAGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.08 . . . . . -710 1 87863470 87863470 C/NA/NA/NA CGCCCCATCCCCTGTGTCTCACCTTTGGCTCCCCCTGGGCTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.13 . . . . . -711 1 8818914 8818914 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 9 1.1210e-01 . . -712 1 89108561 89108570 TTTGTTGTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.75 10.26 . . . . . -713 1 89205442 89205442 T/NA/NA/NA TCTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 16.27 8.94 . . . . . -714 1 89298924 89298924 C/NA/NA/NA CTGAAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.02 9.46 . . . . . -715 1 89310538 89310542 CAAAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.000 25.75 7.48 . . . . . -716 1 8980238 8980239 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -717 1 90026153 90026167 ATCTCATTGTTCAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 44.89 -1.614 3.58 6.74 . . . . . -718 1 90228194 90228196 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.53 7.10 . . . . . -719 1 9038731 9038731 NA/A/A/NA NA/AAAC/AAAAC/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 38.00 -720 1 9038731 9038731 NA/A/A/NA NA/AAAAC/AAAAC/NA FALSE FALSE TRUE FALSE . . . . 4 . . 0.00000 38.00 -721 1 90845810 90845812 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.11 6.73 . . . . . -722 1 9102468 9102470 ATG/NA/NA/ATG A/NA/NA/A FALSE FALSE FALSE TRUE 60.00 0.000 11.43 5.83 . 11 7.3657e-02 . . -723 1 91092921 91092925 GTTAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 19.85 7.67 . . . . . -724 1 91134042 91134043 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.42 3.170 11.13 47.36 . . . . . -725 1 9119186 9119190 NA/NA/CCTTT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01332 3.00 -726 1 91194750 91194750 G/NA/NA/NA GAACAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.88 13.23 . . . . . -727 1 91194752 91194752 G/NA/NA/NA GTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.88 13.23 . . . . . -728 1 91669881 91669893 AAAATAAATAAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.03 0.228 12.69 7.77 . . . . . -729 1 919994 919998 A/A/ATTTA/NA ATTTCTTTCTTTC/ATTTCTTTCTTTCTTTCTTTCTTTC/TATTTCTTTCTTTCTTTCTTTCTTTCTTCC/NA FALSE FALSE TRUE FALSE 60.88 . 1.01 13.86 24 . . 0.00000 11.00 -730 1 922666 922666 NA/C/C/C NA/CTTTTT/CTTTTTTT/CTTTT FALSE FALSE TRUE FALSE . . . . 5 0 9.1950e-01 0.00000 23.00 -731 1 922666 922666 NA/C/C/C NA/CTTTT/CTTTTTTT/CTTTT FALSE FALSE TRUE FALSE . . . . 4 0 9.1950e-01 0.00000 23.00 -732 1 92743421 92743421 C/NA/NA/NA CATGACCTCTCCCTTTGCTTAAAGAAAAGCTGTAAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.94 6.35 . . . . . -733 1 92891010 92891010 T/NA/NA/NA TG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.20 13.38 . . . . . -734 1 93223310 93223310 T/NA/NA/NA TAAAACTCAAAACTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.88 13.65 . . . . . -735 1 9385283 9385289 NA/NA/CACCCCC/NA NA/NA/TACCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 13.00 -736 1 9416962 9416962 NA/NA/G/NA NA/NA/AGATGAGTGAATAATGGATGGATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 -737 1 9439843 9439848 NA/GAAAGA/GA/NA NA/G/G/NA FALSE FALSE TRUE FALSE . . . . 5 . . 0.00377 4.00 -738 1 94824 94826 NA/NA/NA/CTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 10 9.3883e-02 . . -739 1 951440 951441 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 12 5.6683e-02 . . -740 1 9550378 9550378 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -741 1 95572410 95572410 C/NA/NA/NA CCAATTTTTGGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.50 8.87 . . . . . -742 1 9559353 9559354 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.17512 11.00 -743 1 96177553 96177553 G/NA/NA/NA GGATAAATATTCTTTTGCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.52 9.01 . . . . . -744 1 96185056 96185056 T/NA/NA/NA TCTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.15 8.71 . . . . . -745 1 96384544 96384544 C/NA/NA/NA CTGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 9.46 . . . . . -746 1 964745 964745 NA/NA/A/NA NA/NA/ATCTATGCAGGCAGGTAGGGGGATCAGTG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04384 1.00 -747 1 9684705 9684705 NA/C/C/C NA/CTTT/CTTTTT/CTT FALSE FALSE TRUE FALSE . . . . 3 2 5.2930e-01 0.00000 24.00 -748 1 9684705 9684705 NA/C/C/C NA/CTT/CTTTTT/CTT FALSE FALSE TRUE FALSE . . . . 2 2 5.2930e-01 0.00000 24.00 -749 1 97132272 97132272 T/NA/NA/NA TAATCATATACATCTAGTATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.80 8.66 . . . . . -750 1 97167512 97167512 A/NA/NA/NA ATTTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.05 9.13 . . . . . -751 1 97234858 97234858 A/NA/NA/NA AGCAGTCAGAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.66 9.46 . . . . . -752 1 97238365 97238365 A/NA/NA/NA AGAATAGGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.87 9.88 . . . . . -753 1 97348958 97348962 CTATT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.10 10.000 23.43 10.26 . . . . . -754 1 9740505 9740505 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 8 1.5766e-01 . . -755 1 9744960 9744960 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -756 1 97456393 97456393 A/NA/NA/NA AACTACATAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.46 9.21 . . . . . -757 1 9771638 9771639 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . -758 1 9810773 9810773 NA/NA/C/NA NA/NA/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00008 0.00 -759 1 98413333 98413333 A/NA/NA/NA AACATTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.29 8.71 . . . . . -760 1 98660552 98660552 G/NA/NA/NA GTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.46 . . . . . -761 1 99224314 99224314 G/NA/NA/NA GATATATAATAATAATAGCCTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 8.60 . . . . . -762 1 99248350 99248350 A/NA/NA/NA ATTTTAGTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.84 9.36 . . . . . -763 1 9995188 9995189 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 9 1.1105e-01 . . -764 1 99968642 99968642 G/NA/NA/NA GGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.76 8.44 . . . . . -765 1 9999600 9999600 NA/NA/C/NA NA/NA/CTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 25.00 +X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs FILTER_Mutect2 FILTER_Freebayes FILTER_Vardict FILTER_Varscan m2_MQ m2_MQRankSum m2_NLOD m2_TLOD f_LEN vs_SSC vs_SPV vd_SSF vd_MSI vd_SOR +1 1 100202139 100202139 C/NA/NA/NA CTTAAAAAAATA/NA/NA/NA TRUE FALSE FALSE FALSE 59.29 0.449 5.74 6.44 . . . . . . +2 1 10022735 10022736 NA/GT/NA/G NA/G/NA/GT FALSE FALSE FALSE TRUE . . . . 1 14 3.5518e-02 . . . +3 1 10022735 10022736 NA/GT/NA/G NA/GTT/NA/GT FALSE FALSE FALSE TRUE . . . . 1 14 3.5518e-02 . . . +4 1 10041925 10041926 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 13 4.9053e-02 . . . +5 1 100448319 100448319 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 12.22 . . . . . . +6 1 100448320 100448320 G/NA/NA/NA GATATACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 12.22 . . . . . . +7 1 101241945 101241945 A/NA/NA/NA AAAGTCATATGACTCACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.78 9.21 . . . . . . +8 1 101273498 101273498 A/NA/NA/NA ATCACTTGCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.65 11.94 . . . . . . +9 1 101273500 101273500 T/NA/NA/NA TAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.63 11.95 . . . . . . +10 1 101338625 101338625 T/NA/NA/NA TAGGCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 9.17 . . . . . . +11 1 101386745 101386749 TAGAG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.02 . . . . . . +12 1 1014360 1014361 NA/NA/GG/NA NA/NA/CC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.26520 6.00 0.00000 +13 1 101525739 101525739 A/NA/NA/NA ACCAGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.84 12.40 . . . . . . +14 1 10179 10179 NA/NA/NA/C NA/NA/NA/CCT FALSE FALSE FALSE TRUE . . . . . 3 4.0441e-01 . . . +15 1 10210 10211 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 3 4.3590e-01 . . . +16 1 10212317 10212317 NA/A/A/A NA/AAAT/AAAT/AAAT FALSE FALSE FALSE TRUE . . . . 3 19 1.1346e-02 0.07404 13.00 0.30266 +17 1 102315720 102315720 A/NA/NA/NA AGTTATGCTTC/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.000 8.80 8.74 . . . . . . +18 1 102327622 102327622 A/NA/NA/NA AATGTTGAAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 8.71 . . . . . . +19 1 102513289 102513289 G/NA/NA/NA GTTGGGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.98 9.82 . . . . . . +20 1 102572520 102572520 G/NA/NA/NA GGCTAAGATCAAGTATAGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.46 9.26 . . . . . . +21 1 10267337 10267337 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 13 4.3453e-02 . . . +22 1 1028417 1028418 NA/NA/CA/CA NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 17 1.7767e-02 0.00440 11.00 0.00000 +23 1 103307408 103307408 G/NA/NA/NA GGTTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 9.69 . . . . . . +24 1 1034532 1034535 NA/NA/NA/CTAT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.7368e-02 . . . +25 1 10351 10351 NA/NA/NA/C NA/NA/NA/CG FALSE FALSE FALSE TRUE . . . . . 10 9.9617e-02 . . . +26 1 103641570 103641570 A/NA/NA/NA ACGTCAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.12 9.32 . . . . . . +27 1 10366815 10366815 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 7 1.6221e-01 . . . +28 1 103774297 103774297 A/NA/NA/NA AATAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.69 . 14.33 12.04 . . . . . . +29 1 103784492 103784492 T/NA/NA/NA TTAACACTTCGATCAGTGAGAATACC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.48 8.73 . . . . . . +30 1 104033649 104033651 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.24 6.76 . . . . . . +31 1 10408837 10408838 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +32 1 104134500 104134500 A/NA/NA/NA AGAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.61 7.93 . . . . . . +33 1 10469706 10469706 NA/NA/C/NA NA/NA/CTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00004 33.00 0.00000 +34 1 104809335 104809335 A/NA/NA/NA AACTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 8.80 . . . . . . +35 1 104910369 104910369 T/NA/NA/NA TGCAGAATAAACAAGTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.32 11.90 . . . . . . +36 1 10491895 10491895 NA/A/A/A NA/AGCGAGACTCC/AGCGAGACTCC/AGCGAGACTCC FALSE TRUE FALSE TRUE . . . . 10 22 5.3875e-03 0.85482 2.00 0.89523 +37 1 10491912 10491912 NA/G/NA/G NA/GA/NA/GA FALSE FALSE FALSE TRUE . . . . 1 23 4.8664e-03 . . . +38 1 10495773 10495773 T/NA/NA/NA TACACACACACACACACAC/NA/NA/NA TRUE FALSE FALSE FALSE 59.81 . 6.29 6.37 . . . . . . +39 1 105110948 105110948 C/NA/NA/NA CTATTAAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.69 9.63 . . . . . . +40 1 105381264 105381264 T/NA/NA/NA TATGTGGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.42 9.01 . . . . . . +41 1 105461037 105461037 A/NA/NA/NA ATATGTTT/NA/NA/NA TRUE FALSE FALSE FALSE 59.79 0.263 11.74 8.84 . . . . . . +42 1 105497136 105497136 A/NA/NA/NA ATAATGATTTAGAATTTTAGGAAAATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.04 9.09 . . . . . . +43 1 10562853 10562855 NA/CTT/CTT/CTT NA/C/C/C FALSE FALSE FALSE TRUE . . . . 2 35 2.6466e-04 0.00149 17.00 0.15094 +44 1 105687075 105687075 A/NA/NA/NA ATTGTTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.08 9.05 . . . . . . +45 1 10606761 10606762 NA/GA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +46 1 106342981 106342981 T/NA/NA/NA TTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 8.77 . . . . . . +47 1 1066810 1066810 NA/NA/C/NA NA/NA/CTTTTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 20.00 0.00000 +48 1 106845263 106845263 T/NA/NA/NA TACTTAAGGAATTGCAAATTAAAATAACCCATAAGATACTATTATATACTTATTAGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.71 9.21 . . . . . . +49 1 10718053 10718054 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 8 1.3663e-01 . . . +50 1 107922569 107922569 A/NA/NA/NA AGTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.26 . . . . . . +51 1 108231459 108231459 A/NA/NA/NA AACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.46 8.84 . . . . . . +52 1 108430247 108430254 AATCTTTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.12 9.47 . . . . . . +53 1 10854233 10854235 NA/CGT/NA/CGT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 2 5 2.5692e-01 . . . +54 1 10857307 10857308 NA/TG/TG/TG NA/T/T/T FALSE FALSE TRUE TRUE . . . . 1 10 8.9571e-02 0.14923 10.00 0.00000 +55 1 10877986 10877986 NA/NA/T/NA NA/NA/TTCTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 5.00 0.00000 +56 1 109053538 109053538 C/NA/NA/NA CTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.16 9.26 . . . . . . +57 1 109317925 109317925 A/NA/NA/NA AGAATTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 8.88 . . . . . . +58 1 10943746 10943746 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.93 6.75 . . . . . . +59 1 10943747 10943747 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.93 6.74 . . . . . . +60 1 10989988 10989989 NA/CA/NA/CA NA/CAA/NA/C FALSE FALSE FALSE TRUE . . . . 1 19 1.0837e-02 . . . +61 1 10989988 10989989 NA/CA/NA/CA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 19 1.0837e-02 . . . +62 1 110447824 110447827 CTAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.57 6.70 . . . . . . +63 1 11068690 11068694 CATAA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.78 7.50 . . . . . . +64 1 11094454 11094455 NA/NA/TA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03863 12.00 0.00000 +65 1 11099792 11099792 NA/NA/G/NA NA/NA/GA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02825 2.00 0.00000 +66 1 11101803 11101803 NA/NA/G/NA NA/NA/GTGGATGGATAGATAGATGGCTGGAAGGATGGATTAATGGGTGGATTGATGGATGGGTAGGATTGGTAGGTAGAAGGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00043 3.00 0.00000 +67 1 11138321 11138322 NA/CT/CT/CT NA/C/C/C FALSE TRUE TRUE TRUE . . . . 1 15 2.6475e-02 0.00288 11.00 0.00000 +68 1 11170050 11170050 NA/C/C/C NA/CAA/CA/CA FALSE FALSE FALSE TRUE . . . . 2 18 1.2694e-02 0.01059 18.00 0.07968 +69 1 11170050 11170050 NA/C/C/C NA/CA/CA/CA FALSE FALSE FALSE TRUE . . . . 1 18 1.2694e-02 0.01059 18.00 0.07968 +70 1 112091829 112091829 G/NA/NA/NA GATAAGGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.57 9.22 . . . . . . +71 1 11427605 11427605 NA/A/A/NA NA/AT/AT/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.28547 12.00 0.18903 +72 1 11433951 11433951 NA/G/NA/NA NA/GAT/NA/NA FALSE TRUE FALSE FALSE . . . . 2 . . . . . +73 1 11434412 11434412 NA/NA/T/NA NA/NA/TGGTGTGTGTGGTGTGTGGATGATGGATGTGTGTGGATATGGATGTGTGTGGTGTGTGGATATGGATGTGTGTGGTGCATGGATATG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00546 3.00 0.00000 +74 1 114350395 114350397 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 12.79 . . . . . . +75 1 11499557 11499559 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.13 5.773 14.71 6.91 . . . . . . +76 1 115228332 115228332 A/NA/NA/NA AATCAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.10 9.09 . . . . . . +77 1 115403519 115403519 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.02 . . . . . . +78 1 115403520 115403520 A/NA/NA/NA ATACATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.02 . . . . . . +79 1 115403968 115403968 T/NA/NA/NA TAACTATAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.53 9.17 . . . . . . +80 1 116811095 116811095 T/NA/NA/NA TGCCCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 30.43 7.09 . . . . . . +81 1 11700567 11700568 NA/TA/TA/TA NA/T/T/T FALSE FALSE FALSE TRUE . . . . 1 13 4.1862e-02 0.02975 9.00 0.36449 +82 1 11726441 11726441 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 20 8.3090e-03 . . . +83 1 11734353 11734353 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 59.58 -12.381 26.09 9.98 . . . . . . +84 1 118975114 118975114 G/NA/NA/NA GAGAAAGAGCGTCGTGTAGGGAAAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 6.31 . . . . . . +85 1 11906676 11906676 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 26 2.1245e-03 . . . +86 1 11967783 11967783 NA/T/NA/NA NA/TA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +87 1 119930379 119930379 A/NA/NA/NA AGTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.31 . . . . . . +88 1 12021148 12021149 NA/NA/TA/TA NA/NA/T/T FALSE FALSE TRUE TRUE . . . . . 13 4.7727e-02 0.01001 10.00 0.00000 +89 1 12041977 12041977 NA/G/G/NA NA/GTTTTTTT/GTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 7 . . 0.00033 21.00 0.00000 +90 1 12041977 12041977 NA/G/G/NA NA/GT/GTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00033 21.00 0.00000 +91 1 12057936 12057936 NA/NA/C/NA NA/NA/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 28.00 0.00000 +92 1 12076969 12076969 NA/G/G/NA NA/GT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 25.00 0.00000 +93 1 12076969 12076969 NA/G/G/NA NA/GTTT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 25.00 0.00000 +94 1 12076969 12076969 NA/G/G/NA NA/GTT/GTTTTT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 25.00 0.00000 +95 1 12122588 12122588 NA/G/G/NA NA/GCATCCATC/GCATCCATC/NA FALSE FALSE TRUE FALSE . . . . 8 . . 0.01003 10.00 0.00000 +96 1 1224359 1224359 NA/NA/T/T NA/NA/TCC/TCC FALSE FALSE FALSE TRUE . . . . . 4 3.2903e-01 0.22794 5.00 0.00000 +97 1 122949 122949 C/NA/NA/NA CAAAAGTT/NA/NA/NA TRUE FALSE FALSE FALSE 42.38 -2.615 4.21 6.44 . . . . . . +98 1 12349620 12349620 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +99 1 12387978 12387979 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02444 11.00 0.00000 +100 1 12408687 12408688 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.07857 11.00 0.00000 +101 1 12426122 12426122 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 5 2.5714e-01 . . . +102 1 12439825 12439826 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +103 1 12494025 12494028 NA/TGGA/TGGA/TGGA NA/T/T/T FALSE FALSE TRUE TRUE . . . . 3 23 4.5928e-03 0.00001 10.00 0.00000 +104 1 12494025 12494028 NA/TGGA/TGGA/TGGA NA/TGA/T/T FALSE FALSE TRUE TRUE . . . . 1 23 4.5928e-03 0.00001 10.00 0.00000 +105 1 12509191 12509191 NA/G/NA/NA NA/GA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +106 1 12509450 12509450 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +107 1 12519537 12519538 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 14 3.7726e-02 . . . +108 1 12589073 12589074 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +109 1 12635723 12635726 CTAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.29 8.83 . . . . . . +110 1 12783857 12783857 NA/A/A/NA NA/ACTTCTGCCTCCTGGGTTCAAGGGATT/ACTTCAGCCTCCTGGGTTCAAGGGATT/NA FALSE FALSE TRUE FALSE . . . . 26 . . 0.05952 2.00 0.00000 +111 1 12793209 12793209 NA/NA/C/C NA/NA/CTTT/CTTT FALSE FALSE FALSE TRUE . . . . . 19 1.1802e-02 0.01987 16.00 0.24048 +112 1 12800857 12800859 NA/CTT/C/NA NA/CTTTTT/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 25.00 0.00000 +113 1 12800857 12800859 NA/CTT/C/NA NA/C/CTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 25.00 0.00000 +114 1 12849547 12849555 NA/CTCTTTCTT/CTCTTTCTT/CTCTTTCTT NA/C/C/C FALSE FALSE FALSE TRUE . . . . 8 20 8.1185e-03 0.20697 14.00 0.40777 +115 1 12891724 12891744 NA/NA/CACCTGAAACCCAGCTACATG/NA NA/NA/GGCCTGAAACACAGCGACTCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00003 4.00 0.00000 +116 1 13007229 13007229 NA/NA/G/NA NA/NA/GA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02121 11.00 0.00000 +117 1 13051050 13051050 C/NA/NA/NA CACTAGT/NA/NA/NA TRUE FALSE FALSE FALSE 47.09 -1.648 5.75 10.15 . . . . . . +118 1 13116353 13116353 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 11 6.9231e-02 . . . +119 1 13131254 13131255 NA/AT/AT/AT NA/A/A/A FALSE FALSE FALSE TRUE . . . . 1 25 2.6087e-03 0.22559 20.00 0.28255 +120 1 13155619 13155619 G/NA/NA/NA GCATCTACT/NA/NA/NA TRUE FALSE FALSE FALSE 47.62 -0.424 15.01 8.65 . . . . . . +121 1 13168951 13168951 NA/G/G/G NA/GAAGAAAGAAAGA/GAAGAAAGAAAGA/GAAGAAAGAAAGA FALSE FALSE FALSE TRUE . . . . 12 14 3.7589e-02 0.02447 16.00 0.33987 +122 1 13168951 13168951 NA/G/G/G NA/GAAGA/GAAGAAAGAAAGA/GAAGAAAGAAAGA FALSE FALSE FALSE TRUE . . . . 4 14 3.7589e-02 0.02447 16.00 0.33987 +123 1 13177471 13177471 NA/C/C/NA NA/CT/CT/NA FALSE TRUE TRUE FALSE . . . . 1 . . 0.10264 11.00 0.00000 +124 1 1318005 1318005 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 9 1.1029e-01 . . . +125 1 13663076 13663076 NA/G/G/G NA/GAGAAAGAA/GAGAAAGAA/GAGAAAGAA FALSE FALSE FALSE TRUE . . . . 8 16 2.0843e-02 0.00160 18.00 0.00000 +126 1 13774646 13774646 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +127 1 13775521 13775522 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +128 1 13805627 13805627 NA/C/C/C NA/CT/CT/CT FALSE FALSE FALSE TRUE . . . . 1 9 1.2195e-01 0.10638 11.00 0.00000 +129 1 13926866 13926866 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +130 1 13974354 13974355 NA/CA/CA/CA NA/C/C/C FALSE FALSE FALSE TRUE . . . . 1 13 4.1563e-02 0.03168 16.00 0.15362 +131 1 13974354 13974355 NA/CA/CA/CA NA/CAA/C/C FALSE FALSE FALSE TRUE . . . . 1 13 4.1563e-02 0.03168 16.00 0.15362 +132 1 14034316 14034317 NA/CT/NA/CT NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 14 3.5782e-02 . . . +133 1 14126948 14126950 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 6.38 . . . . . . +134 1 14167446 14167458 NA/TATAATAATAATA/TATAATAATAATA/TATAATAATAATA NA/T/T/T FALSE FALSE FALSE TRUE . . . . 12 26 2.0202e-03 0.00905 13.00 0.00000 +135 1 142550392 142550392 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 48.67 -0.834 33.09 11.88 . . . . . . +136 1 142581125 142581127 GTT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 49.52 -3.580 11.47 6.55 . . . . . . +137 1 14262591 14262591 NA/G/G/NA NA/GTTTTTTTTTTT/GTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 11 . . 0.00009 27.00 0.00000 +138 1 14262591 14262591 NA/G/G/NA NA/GTTTTTTTTTTTT/GTTTTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . 12 . . 0.00009 27.00 0.00000 +139 1 142670528 142670530 ACT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 47.29 -1.830 5.89 33.53 . . . . . . +140 1 142918207 142918208 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 46.27 0.133 8.03 7.83 . . . . . . +141 1 14305593 14305594 NA/GA/GA/GA NA/G/G/G FALSE FALSE FALSE TRUE . . . . 1 13 4.7740e-02 0.01442 13.00 0.17723 +142 1 14305593 14305594 NA/GA/GA/GA NA/GAA/G/G FALSE FALSE FALSE TRUE . . . . 1 13 4.7740e-02 0.01442 13.00 0.17723 +143 1 143135392 143135393 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 52.26 -3.070 24.02 12.48 . . . . . . +144 1 143151982 143151982 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 53.40 -2.839 4.37 11.38 . . . . . . +145 1 143158449 143158449 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 53.10 -2.608 67.57 16.69 . . . . . . +146 1 143168922 143168965 ACCTTACTGACAAGGCCTCACTGGCAAGGCCTCACTGACGAGGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.33 -2.220 33.40 7.18 . . . . . . +147 1 14329215 14329215 C/NA/NA/NA CTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.94 8.84 . . . . . . +148 1 143428977 143428977 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 42.35 -1.571 3.93 13.78 . . . . . . +149 1 143482108 143482109 TC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 46.94 -2.025 3.69 24.59 . . . . . . +150 1 143504763 143504763 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 48.42 -0.660 8.88 7.43 . . . . . . +151 1 144579868 144579868 A/NA/NA/NA AATGT/NA/NA/NA TRUE FALSE FALSE FALSE 47.59 -2.513 7.22 6.83 . . . . . . +152 1 144602222 144602222 C/NA/NA/NA CATAAGAATCCTAAGAGA/NA/NA/NA TRUE FALSE FALSE FALSE 44.21 -1.394 3.04 6.44 . . . . . . +153 1 144899410 144899410 G/NA/NA/NA GTTTTTTATATAGT/NA/NA/NA TRUE FALSE FALSE FALSE 59.82 -8.619 11.18 8.91 . . . . . . +154 1 144991389 144991397 TACACACAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 57.56 2.427 7.17 21.71 . . . . . . +155 1 145016034 145016034 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.04 0.000 7.58 30.52 . . . . . . +156 1 145037620 145037620 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 59.38 -1.584 22.83 6.52 . . . . . . +157 1 145040832 145040832 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.95 11.19 . . . . . . +158 1 145110305 145110305 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 36.75 10.05 . . . . . . +159 1 145110306 145110306 A/NA/NA/NA AAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 36.74 10.05 . . . . . . +160 1 145236043 145236049 AGTGTTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 56.06 -3.365 19.81 7.08 . . . . . . +161 1 145250219 145250219 A/NA/NA/NA ATATT/NA/NA/NA TRUE FALSE FALSE FALSE 57.83 -3.866 10.09 8.45 . . . . . . +162 1 145292407 145292408 AC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.91 3.299 11.41 39.80 . . . . . . +163 1 145375050 145375050 C/NA/NA/NA CAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 50.92 -1.251 13.98 7.14 . . . . . . +164 1 145376566 145376566 T/NA/NA/NA TC/NA/NA/NA TRUE FALSE FALSE FALSE 53.17 -3.235 19.71 9.14 . . . . . . +165 1 1454046 1454048 NA/TAC/TAC/NA NA/T/T/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.51471 12.00 0.00000 +166 1 146397483 146397483 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 53.31 -4.536 7.53 10.37 . . . . . . +167 1 146479610 146479610 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 57.38 -7.337 6.77 12.40 . . . . . . +168 1 14662242 14662244 NA/NA/GCA/NA NA/NA/G/NA FALSE FALSE TRUE FALSE . . . . . . . 0.11412 7.00 0.00000 +169 1 14671412 14671413 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +170 1 147025524 147025524 A/NA/NA/NA AGCTAATATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.47 8.97 . . . . . . +171 1 147311506 147311521 TATATGTGAGACATAG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 55.29 -5.289 7.23 6.51 . . . . . . +172 1 147343502 147343502 G/NA/NA/NA GTGTTCTACAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.24 12.65 . . . . . . +173 1 147356904 147356904 C/NA/NA/NA CCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.64 12.88 . . . . . . +174 1 148001285 148001285 G/NA/NA/NA GA/NA/NA/NA TRUE FALSE FALSE FALSE 51.20 0.392 16.90 11.21 . . . . . . +175 1 148352296 148352298 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.41 0.000 4.41 14.39 . . . . . . +176 1 148849102 148849128 TCATTTCATTTCCTCATTTCATTTCAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 53.68 0.587 3.56 28.85 . . . . . . +177 1 148849397 148849402 ACATTT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 51.79 -3.993 29.69 28.14 . . . . . . +178 1 149338550 149338550 T/NA/NA/NA TGTGTTAGTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 54.30 -3.043 10.23 6.65 . . . . . . +179 1 14949185 14949186 NA/CA/C/NA NA/C/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 0.00 0.00000 +180 1 14949185 14949186 NA/CA/C/NA NA/CAAAAAAAA/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 7 . . 0.00000 0.00 0.00000 +181 1 149857497 149857497 A/NA/NA/NA AATAATCCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 -0.099 15.09 7.80 . . . . . . +182 1 149857499 149857499 G/NA/NA/NA GCACTTTGAGAGACCAAGGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 -0.099 15.09 7.80 . . . . . . +183 1 149879052 149879066 ATATTCTATTACAGG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.38 8.69 . . . . . . +184 1 1501010 1501010 NA/NA/G/NA NA/NA/GTGGGCTCCATGGGAACCGAGACCCAACACCCAAAGGAGTCCCACAGGCTCAGGGGTGGTGCAGGCAGAGAACAGACGTCGCGATGGGCCCGACGGTGC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +185 1 150256413 150256416 TTTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.280 9.63 19.03 . . . . . . +186 1 150356926 150356932 CATTATT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 . 12.76 7.67 . . . . . . +187 1 150360955 150360957 CTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.95 8.94 . . . . . . +188 1 15062748 15062748 NA/NA/A/A NA/NA/AGG/AGG FALSE FALSE FALSE TRUE . . . . . 10 9.5238e-02 0.57946 5.00 0.43302 +189 1 15089357 15089360 CAAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.76 10.77 . . . . . . +190 1 150908053 150908053 C/NA/NA/NA CCTCGGCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 8.83 . . . . . . +191 1 15116656 15116656 T/NA/NA/NA TCTGTAATGATACCCACAGACTCAAAGTAAAAGGATGGAGAAAGGTTTG/NA/NA/NA TRUE FALSE FALSE FALSE 59.59 0.000 16.56 6.37 . . . . . . +192 1 151326041 151326041 G/NA/NA/NA GACCA/NA/NA/NA TRUE FALSE FALSE FALSE 59.47 -7.093 12.05 10.57 . . . . . . +193 1 15176434 15176435 NA/CT/CT/CT NA/C/C/C FALSE TRUE FALSE TRUE . . . . 1 21 7.0648e-03 0.00184 14.00 0.00000 +194 1 152106280 152106281 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.53 7.52 . . . . . . +195 1 15236546 15236546 NA/C/C/C NA/CAATA/CAATA/CAATA FALSE FALSE TRUE TRUE . . . . 4 22 5.4987e-03 0.00704 4.00 0.00000 +196 1 152863578 152863581 AAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.85 10.54 . . . . . . +197 1 152974408 152974408 G/NA/NA/NA GTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 13.23 . . . . . . +198 1 152989728 152989728 T/NA/NA/NA TATATACGTGTATATATATATACATATACACGTATATACGTGTATATATATACATATACACGTATATACGTGTATATATATATAC/NA/NA/NA TRUE FALSE FALSE FALSE 57.02 -4.628 3.87 14.24 . . . . . . +199 1 15319663 15319664 NA/TA/NA/TA NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 1 18 1.4475e-02 . . . +200 1 15332287 15332288 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +201 1 153861447 153861447 A/NA/NA/NA AACTACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.06 9.45 . . . . . . +202 1 15427660 15427660 NA/T/T/T NA/TTCTCTCTCTC/TTCTCTCTCTCTCTCTCTCTCTCTC/TTCTCTCTCTC FALSE FALSE TRUE FALSE . . . . 10 1 7.4954e-01 0.00004 23.00 0.00000 +203 1 154331579 154331581 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.13 6.33 . . . . . . +204 1 154357184 154357188 AAAAC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.70 6.33 . . . . . . +205 1 154694454 154694454 G/NA/NA/NA GAGCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 16.26 9.01 . . . . . . +206 1 155095812 155095815 CTTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.12 11.21 . . . . . . +207 1 15554510 15554512 NA/NA/NA/TTG NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 12 6.1668e-02 . . . +208 1 155634552 155634552 A/NA/NA/NA AGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.36 . . . . . . +209 1 155634553 155634553 A/NA/NA/NA AGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.36 . . . . . . +210 1 15572956 15572979 NA/NA/AGATAGGATTTCCTGCTGGAGATA/NA NA/NA/TTGCTCTGCCCTCAAGTAGAAGTGGGAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +211 1 15598102 15598102 NA/NA/T/NA NA/NA/TGGAAATAACTAATCGCATG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00042 3.00 0.00000 +212 1 15604971 15604971 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 22 5.1847e-03 . . . +213 1 15629213 15629214 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +214 1 15635778 15635782 GATTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.49 6.45 . . . . . . +215 1 15641171 15641171 NA/NA/T/NA NA/NA/TGGGTGTAAGCATAGGGGGTGTATGGGTGTGAGTATGGGGGGAGTATGTATGGGTGTGTGGGGTGTGTGTGGATGTGTGGGTGAGGGTGTTGGGAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +216 1 15641246 15641246 NA/NA/G/NA NA/NA/GTGGATGTGTGTGGGTATGTGGGGGGTGTGGGAGTGTGGAGATGTATGAGTGTGGGTGTGTGAGAGGGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00238 4.00 0.00000 +217 1 156682152 156682154 GGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.54 6.84 . . . . . . +218 1 15710494 15710496 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 26.62 9.04 . . . . . . +219 1 157761187 157761187 G/NA/NA/NA GCTGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 15.84 . . . . . . +220 1 15781658 15781658 NA/A/A/NA NA/AC/AC/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 40.00 0.00000 +221 1 15781702 15781703 NA/NA/NA/TC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 9 1.1565e-01 . . . +222 1 15790384 15790385 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +223 1 157966837 157966845 GACTAAGTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 28.28 7.42 . . . . . . +224 1 15821357 15821358 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 18 1.3082e-02 . . . +225 1 158675701 158675701 A/NA/NA/NA AGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.51 8.84 . . . . . . +226 1 158685987 158685987 T/NA/NA/NA TGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.23 9.09 . . . . . . +227 1 158839725 158839725 G/NA/NA/NA GCTA/NA/NA/NA TRUE FALSE FALSE FALSE 58.77 -4.900 12.64 6.33 . . . . . . +228 1 158871726 158871726 T/NA/NA/NA TTTTCGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 12.71 . . . . . . +229 1 15896892 15896892 G/NA/NA/NA GCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 9.36 . . . . . . +230 1 15913105 15913106 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 13 4.4382e-02 . . . +231 1 159387827 159387828 GA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.60 52.16 . . . . . . +232 1 1594841 1594841 NA/NA/A/NA NA/NA/CTCGACGGGGAGGTGGACAAGG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +233 1 159622056 159622058 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 10.35 . . . . . . +234 1 160222308 160222308 T/NA/NA/NA TAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.14 12.88 . . . . . . +235 1 16024292 16024293 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.12354 12.00 0.16751 +236 1 160247155 160247166 AGCACACAGTGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.46 9.10 . . . . . . +237 1 160991956 160991960 ATTGT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 20.40 7.75 . . . . . . +238 1 160993666 160993666 C/NA/NA/NA CTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.39 -0.313 15.79 8.05 . . . . . . +239 1 16140640 16140642 NA/CAA/CAA/CA NA/CA/C/C FALSE FALSE FALSE TRUE . . . . 1 13 4.2297e-02 0.08765 18.00 0.45922 +240 1 16140640 16140642 NA/CAA/CAA/CA NA/C/C/C FALSE FALSE FALSE TRUE . . . . 2 13 4.2297e-02 0.08765 18.00 0.45922 +241 1 161414339 161414341 GTC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 36.25 -0.848 3.49 22.15 . . . . . . +242 1 16155538 16155539 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 2.5348e-02 . . . +243 1 161664777 161664777 T/NA/NA/NA TCCCCG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.17 9.05 . . . . . . +244 1 1616853 1616853 NA/NA/G/G NA/NA/AAAA/GA FALSE FALSE TRUE FALSE . . . . . 4 3.2372e-01 0.00026 0.00 0.00000 +245 1 16187104 16187104 NA/C/NA/C NA/CT/NA/CT FALSE TRUE FALSE TRUE . . . . 1 13 3.9989e-02 . . . +246 1 16191915 16191917 NA/GTT/NA/G NA/GTTT/NA/GT FALSE FALSE FALSE TRUE . . . . 1 13 4.4097e-02 . . . +247 1 16191915 16191917 NA/GTT/NA/G NA/G/NA/GT FALSE FALSE FALSE TRUE . . . . 2 13 4.4097e-02 . . . +248 1 16218507 16218508 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 3.0302e-02 . . . +249 1 16218507 16218508 NA/CT/NA/CT NA/CTT/NA/C FALSE FALSE FALSE TRUE . . . . 1 15 3.0302e-02 . . . +250 1 16231386 16231387 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +251 1 162493357 162493357 G/NA/NA/NA GCATACAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 9.25 . . . . . . +252 1 162782394 162782394 G/NA/NA/NA GTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 59.49 -7.809 14.45 6.44 . . . . . . +253 1 16293437 16293437 NA/NA/C/NA NA/NA/CA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02372 11.00 0.00000 +254 1 16297851 16297851 NA/NA/C/NA NA/NA/CACACTATATATATAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.08904 5.00 0.00000 +255 1 16308412 16308412 NA/NA/A/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00008 0.00 0.00000 +256 1 163177630 163177630 A/NA/NA/NA ATGACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.16 6.57 . . . . . . +257 1 163239608 163239609 AT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.82 9.38 . . . . . . +258 1 163681702 163681702 A/NA/NA/NA ATGTGGTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.57 12.99 . . . . . . +259 1 163681703 163681703 A/NA/NA/NA AATTTGTATTTTTCTGATGATAGTGATGGTTGAGTATCTTTTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.57 12.99 . . . . . . +260 1 16382828 16382834 NA/NA/TCTTCCT/NA NA/NA/ACCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00142 4.00 0.00000 +261 1 16388757 16388766 NA/NA/ACCCATCCCC/NA NA/NA/CCCT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00006 6.00 0.00000 +262 1 164128083 164128084 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.73 6.80 . . . . . . +263 1 164145929 164145930 GT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.83 -0.393 8.97 49.45 . . . . . . +264 1 164349942 164349942 A/NA/NA/NA ACATATCCCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.55 9.09 . . . . . . +265 1 1643570 1643572 NA/NA/NA/CAA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 4 3.3088e-01 . . . +266 1 164621971 164621971 A/NA/NA/NA AAAATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 9.26 . . . . . . +267 1 164621972 164621972 C/NA/NA/NA CCAATAATATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 9.26 . . . . . . +268 1 164885488 164885488 C/NA/NA/NA CCAAAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.75 13.08 . . . . . . +269 1 1649112 1649163 NA/NA/GCTCTCTCTGGTTTTCGGTCTGTGACACACGCACACTTTCAGCTGGAGTATC/NA NA/NA/G/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00583 2.00 0.00000 +270 1 1651074 1651077 NA/NA/AGAC/NA NA/NA/TAAACCCGCTCTGTCACCCAGGCT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 19.00 0.00000 +271 1 16517823 16517825 NA/NA/NA/GGA NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 6 2.1429e-01 . . . +272 1 165832980 165832980 G/NA/NA/NA GAAACAATAATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.38 8.87 . . . . . . +273 1 16636855 16636856 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.32524 11.00 0.40515 +274 1 16668104 16668105 NA/TA/NA/TA NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 1 19 1.0366e-02 . . . +275 1 16697888 16697902 CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG/CCTCCCCTCCCTCTG C/C/C/C TRUE TRUE FALSE TRUE 58.21 2.381 3.54 26.86 14 16 2.5045e-02 0.00000 4.00 0.02436 +276 1 16776783 16776783 NA/NA/NA/G NA/NA/NA/GT FALSE FALSE FALSE TRUE . . . . . 7 1.6944e-01 . . . +277 1 167871740 167871740 G/NA/NA/NA GACCTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.85 9.09 . . . . . . +278 1 167965998 167965998 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 8.94 . . . . . . +279 1 167966000 167966001 GC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.94 8.94 . . . . . . +280 1 16840566 16840566 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 55.98 -1.492 13.04 17.04 . . . . . . +281 1 16842744 16842745 GC/NA/NA/GC G/NA/NA/G FALSE FALSE FALSE TRUE 56.43 -0.750 34.13 25.24 . 14 3.9759e-02 . . . +282 1 16849776 16849778 CCA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 56.32 -9.856 8.77 7.36 . . . . . . +283 1 169029403 169029403 C/NA/NA/NA CTTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.26 6.83 . . . . . . +284 1 169209503 169209503 G/NA/NA/NA GTTTGAGAACTTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 9.57 . . . . . . +285 1 16923136 16923138 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 59.45 -6.397 40.97 7.28 . . . . . . +286 1 16933623 16933628 NA/GAAGAA/GAAGAA/GAAGAA NA/G/G/G FALSE FALSE FALSE TRUE . . . . 5 18 1.4683e-02 0.05902 4.00 0.43083 +287 1 16955682 16955693 NA/ATTTTTTTTTTT/A/ATTTTTTTTTTT NA/A/ATTTTTTTTTT/A FALSE FALSE TRUE FALSE . . . . 11 0 8.4047e-01 0.00000 31.00 0.00000 +288 1 16955682 16955693 NA/ATTTTTTTTTTT/A/ATTTTTTTTTTT NA/ATTTTTTTTTTTT/ATTTTTTTTTT/A FALSE FALSE TRUE FALSE . . . . 1 0 8.4047e-01 0.00000 31.00 0.00000 +289 1 16965863 16965863 NA/NA/NA/A NA/NA/NA/ACAGCAG FALSE FALSE FALSE TRUE . . . . . 14 3.8507e-02 . . . +290 1 16970870 16970870 G/NA/G/G GC/NA/GC/GC FALSE FALSE FALSE TRUE 59.77 0.696 2.76 21.32 . 15 2.9144e-02 0.21744 4.00 0.66653 +291 1 16978192 16978193 AC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 57.64 -2.826 6.84 14.93 . . . . . . +292 1 169883560 169883560 A/NA/NA/NA AATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.55 9.09 . . . . . . +293 1 17007961 17007961 NA/A/NA/A NA/AC/NA/AC FALSE FALSE FALSE TRUE . . . . 1 16 2.4913e-02 . . . +294 1 170215106 170215106 T/NA/NA/NA TTATATATTTTAGTTATTAACC/NA/NA/NA TRUE FALSE FALSE FALSE 59.45 0.000 5.20 9.51 . . . . . . +295 1 17030009 17030011 GGT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.02 -0.168 34.59 11.80 . . . . . . +296 1 17034808 17034808 NA/NA/C/NA NA/NA/CTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 32.00 0.00000 +297 1 17051738 17051747 NA/CAGCTTCTGG/CAGCTTCTGG/CAGCTTCTGG NA/C/C/C FALSE TRUE FALSE TRUE . . . . 9 102 5.0170e-11 0.30992 2.00 0.52861 +298 1 17053771 17053774 NA/NA/NA/TGTG NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 29 1.0966e-03 . . . +299 1 170586144 170586144 A/NA/NA/NA ATACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.96 9.22 . . . . . . +300 1 17060199 17060200 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 38.22 -1.631 12.93 31.02 . . . . . . +301 1 170672812 170672812 T/NA/NA/NA TCAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.05 9.05 . . . . . . +302 1 170700350 170700350 C/NA/NA/NA CCTCTTGTATCTTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.18 . . . . . . +303 1 17084729 17084730 CG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 52.31 0.315 18.45 8.14 . . . . . . +304 1 17190073 17190074 NA/NA/CT/NA NA/NA/TC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00149 1.00 0.04841 +305 1 171950789 171950789 G/NA/NA/NA GAGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 9.09 . . . . . . +306 1 171968245 171968245 G/NA/NA/NA GGGCCCCTTTCAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 9.26 . . . . . . +307 1 17202553 17202561 GTTTGTTTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 55.99 -3.068 3.35 28.43 . . . . . . +308 1 17217939 17217941 NA/NA/NA/TTC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 40 9.7149e-05 . . . +309 1 172221200 172221200 T/NA/NA/NA TCTGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.95 8.54 . . . . . . +310 1 172508758 172508758 A/NA/NA/NA AAGAGATTTCATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.40 8.60 . . . . . . +311 1 172555560 172555560 G/NA/NA/NA GAAAGTAATATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.31 6.51 . . . . . . +312 1 17261387 17261389 NA/CTT/CTT/CTT NA/C/C/C FALSE FALSE FALSE TRUE . . . . 2 21 6.9906e-03 0.04005 18.00 0.30237 +313 1 172809799 172809801 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.10 6.64 . . . . . . +314 1 173121421 173121423 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.66 7.04 . . . . . . +315 1 17325900 17325901 NA/AG/AG/NA NA/A/A/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00007 25.00 0.00000 +316 1 173354278 173354278 T/NA/NA/NA TAAAAATTTATATTTAACATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.87 9.13 . . . . . . +317 1 17358699 17358700 NA/CT/NA/CT NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 16 2.2127e-02 . . . +318 1 173630187 173630189 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.20 6.86 . . . . . . +319 1 173657492 173657494 CCT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 58.89 0.000 7.19 13.13 . . . . . . +320 1 17376802 17376803 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04283 12.00 0.00000 +321 1 17430926 17430926 NA/NA/C/NA NA/NA/CTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 30.00 0.00000 +322 1 174698334 174698334 T/NA/NA/NA TTTGCTTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.54 9.17 . . . . . . +323 1 175504583 175504589 TTTGTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.88 0.000 13.64 11.68 . . . . . . +324 1 175922387 175922387 A/NA/NA/NA ATTCACCATTTCTCACAATATTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 8.96 . . . . . . +325 1 175956278 175956278 A/NA/NA/NA ATTGGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.22 9.31 . . . . . . +326 1 175956279 175956279 A/NA/NA/NA ATGTGGTATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.22 9.31 . . . . . . +327 1 17601931 17601931 NA/NA/C/NA NA/NA/AAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 0.00 0.00000 +328 1 177083556 177083558 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.05 7.91 . . . . . . +329 1 17778899 17778899 T/NA/NA/NA TCCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.92 7.33 . . . . . . +330 1 17778900 17778900 G/NA/NA/NA GCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.93 7.34 . . . . . . +331 1 17792618 17792621 NA/TTTC/NA/TTTC NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 3 30 8.0013e-04 . . . +332 1 17796316 17796323 NA/CAAAAAA/NA/CAAAAAAA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 6 15 2.7199e-02 . . . +333 1 17796316 17796323 NA/CAAAAAAA/NA/CAAAAAAA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 7 15 2.7199e-02 . . . +334 1 177978171 177978171 A/NA/NA/NA ATTGAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.53 9.13 . . . . . . +335 1 17820432 17820433 AT/AT/AT/AT A/A/A/A FALSE FALSE TRUE TRUE 60.19 1.528 4.62 19.01 1 33 4.2311e-04 0.00040 9.00 0.04791 +336 1 178801484 178801484 A/NA/NA/NA ATAGTTATGTGACATAGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 8.94 . . . . . . +337 1 179379992 179379992 A/NA/NA/NA AATTTACACT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.24 9.51 . . . . . . +338 1 18015976 18015976 NA/C/C/NA NA/CCT/CCT/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.24026 4.00 0.00000 +339 1 1804495 1804495 NA/G/NA/NA NA/GT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +340 1 18081080 18081081 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 3 4.2118e-01 . . . +341 1 18194209 18194209 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +342 1 1835890 1835893 NA/NA/TATA/NA NA/NA/AT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00210 6.00 0.00000 +343 1 1841664 1841665 NA/AT/AT/AT NA/A/A/A FALSE TRUE FALSE TRUE . . . . 1 16 2.1346e-02 0.03927 11.00 0.09151 +344 1 1866058 1866092 TTGTAGGTACACACGTGTGTACGTGGGTGTTAGGC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 56.94 -0.054 6.18 28.25 . . . . . . +345 1 18762800 18762801 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 8 1.4170e-01 . . . +346 1 18804792 18804792 NA/A/A/A NA/AAC/AAC/AC FALSE FALSE FALSE TRUE . . . . 2 10 8.3333e-02 0.70621 16.00 0.71315 +347 1 18831510 18831512 TGA/NA/NA/TGA T/NA/NA/T FALSE FALSE FALSE TRUE 60.00 0.000 5.40 4.87 . 7 1.8347e-01 . . . +348 1 18881072 18881073 NA/NA/AT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03699 11.00 0.00000 +349 1 18983896 18983897 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.04427 11.00 0.16189 +350 1 19070951 19070951 NA/NA/T/NA NA/NA/TGGATGGATGGATGATGGATGGGTGGATGAGGGATGGATAGAGGATGGATGGATAGAAGGATGGATGGATAGAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00039 13.00 0.00000 +351 1 19124603 19124603 NA/C/C/C NA/CCCCG/CCCCG/CCCCG FALSE FALSE FALSE TRUE . . . . 4 5 2.9371e-01 0.08148 10.00 3.29593 +352 1 19256151 19256160 NA/NA/ACTTGAGAGG/NA NA/NA/GGCCAACAGGACT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00005 2.00 0.00000 +353 1 19262194 19262194 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 14 3.3824e-02 . . . +354 1 1928861 1928862 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +355 1 19484946 19484947 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.02878 11.00 0.07812 +356 1 19628182 19628183 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.03406 12.00 0.00000 +357 1 1963054 1963089 NA/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT/GCTGCAGGACCCAGGTGTCTGGGGCGCTACCATCCT NA/G/G/G FALSE FALSE FALSE TRUE . . . . 35 24 3.3714e-03 0.06812 2.00 0.30238 +358 1 19777212 19777219 AAACTATC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.62 12.71 . . . . . . +359 1 19863459 19863459 NA/NA/G/NA NA/NA/ATATATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00132 0.00 0.00000 +360 1 19873193 19873193 NA/T/NA/NA NA/TA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +361 1 20032285 20032286 NA/GA/GA/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.09528 11.00 0.14431 +362 1 20068231 20068231 NA/C/NA/C NA/CT/NA/CT FALSE FALSE FALSE TRUE . . . . 1 13 4.2825e-02 . . . +363 1 20259424 20259424 NA/NA/A/NA NA/NA/AATCACCATCACCATTAATTATCACCATCAACATCACCATCGGTGCCATCAACATCATCATCATCACCATCACCATCATCATCATCATTACCATTACCATCACCATCATCATCTTCACCATCACCATCACCATTGCACCATCACCATTATCATCATCTTAATCACTATCAACATCACCATAATAATCACC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 3.00 0.00000 +364 1 20346159 20346160 NA/GT/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +365 1 20419641 20419644 ATTC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.98 6.59 . . . . . . +366 1 2055148 2055148 NA/NA/NA/G NA/NA/NA/GGTC FALSE FALSE FALSE TRUE . . . . . 6 2.0420e-01 . . . +367 1 20617658 20617658 NA/A/A/NA NA/AGTGT/AGTGT/NA FALSE FALSE TRUE FALSE . . . . 4 . . 0.03653 8.00 0.00000 +368 1 20619131 20619133 CGT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.29 7.98 . . . . . . +369 1 20708961 20708961 NA/NA/A/A NA/NA/ATGGTGGTGATGGTGGTGATGGTGGTGGTGGGGGGGTAGTGATGGTGGTAATGATTGTGGTGATGGTAGTGGTGATGTTGGTGGTGATGGTGGTGGGGG/ATGG FALSE FALSE TRUE FALSE . . . . . 1 7.8322e-01 0.00007 5.00 0.00000 +370 1 20780714 20780714 NA/NA/T/NA NA/NA/TGTCTATGTGTCTGTGTGTATCTGTGTGTCTGTGTGCTATGTCTGTTTCTGTGTATATGTCCATGTGTGTCTGTGTGTGTATGTCCATGTGTGTCTGTGTATGTGTCCGTGTGTGTTTCCGTGTCTGTTTCTGTGTGTCCGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00260 6.00 0.00000 +371 1 20872180 20872180 A/NA/NA/NA ACATCACATTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.51 9.57 . . . . . . +372 1 20874279 20874280 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6101e-02 . . . +373 1 20934903 20934903 NA/T/T/NA NA/TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGC/TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTAGC/NA FALSE FALSE TRUE FALSE . . . . 35 . . 0.00000 6.00 0.00000 +374 1 20997998 20997998 NA/A/NA/A NA/AT/NA/AT FALSE TRUE FALSE TRUE . . . . 1 15 3.0395e-02 . . . +375 1 21001068 21001068 NA/C/C/C NA/CT/CT/CT FALSE FALSE FALSE TRUE . . . . 1 14 3.2530e-02 0.23206 17.00 0.46323 +376 1 21039143 21039146 NA/NA/NA/ATAT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 4 3.5979e-01 . . . +377 1 21156502 21156502 G/NA/NA/NA GGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.75 8.94 . . . . . . +378 1 2117935 2117935 NA/NA/G/NA NA/NA/GC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.52632 10.00 0.00000 +379 1 21219986 21219986 G/NA/NA/NA GGGGTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.69 13.23 . . . . . . +380 1 21273938 21273939 NA/TA/TA/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.01629 12.00 0.08993 +381 1 21283110 21283110 NA/NA/C/NA NA/NA/AAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00031 0.00 0.00000 +382 1 21306249 21306249 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +383 1 21351940 21351941 NA/NA/GA/GA NA/NA/G/G FALSE FALSE FALSE TRUE . . . . . 9 1.1099e-01 0.11538 10.00 0.00000 +384 1 21367445 21367446 NA/NA/AT/AT NA/NA/A/A FALSE FALSE FALSE TRUE . . . . . 5 2.9247e-01 0.23345 11.00 0.00000 +385 1 21380959 21380959 NA/T/T/NA NA/TA/TA/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.10502 12.00 0.15383 +386 1 21381713 21381725 TGATATTTTGCTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.93 9.10 . . . . . . +387 1 21409980 21409981 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +388 1 21567673 21567673 G/NA/NA/NA GTCTGTTTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.76 7.54 . . . . . . +389 1 21638002 21638002 NA/NA/C/NA NA/NA/AAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +390 1 21728322 21728342 NA/AAAATAAATAAATAAATAAAT/AAAATAAAT/AAAATAAAT NA/A/A/A FALSE FALSE FALSE TRUE . . . . 20 25 3.0782e-03 0.12473 12.00 0.40518 +391 1 21728322 21728330 NA/AAAATAAAT/AAAATAAAT/AAAATAAAT NA/A/A/A FALSE FALSE FALSE TRUE . . . . 8 25 3.0782e-03 0.12473 12.00 0.40518 +392 1 21744993 21744993 NA/NA/A/A NA/NA/AT/AT FALSE FALSE FALSE TRUE . . . . . 13 4.8364e-02 0.07824 2.00 0.00000 +393 1 21745022 21745022 NA/A/A/NA NA/ATGTATGTGTATGTGT/GTGT/NA FALSE FALSE TRUE FALSE . . . . 15 . . 0.00312 0.00 0.00000 +394 1 21745022 21745022 NA/A/A/NA NA/ATGTATATGTATATGT/GTGT/NA FALSE FALSE TRUE FALSE . . . . 15 . . 0.00312 0.00 0.00000 +395 1 21766605 21766611 NA/TGCAGGC/TGCAGGC/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 6 . . 0.40000 4.00 0.00000 +396 1 22027858 22027858 NA/NA/C/C NA/NA/CA/CA FALSE FALSE FALSE TRUE . . . . . 13 4.6726e-02 0.08478 17.00 0.43874 +397 1 22045057 22045057 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +398 1 22051593 22051593 T/NA/NA/NA TTGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.83 13.08 . . . . . . +399 1 22098301 22098301 NA/NA/G/NA NA/NA/GC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 1.00 0.00000 +400 1 22286329 22286379 NA/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG/ACGGTGGCCCATGCCTGTAATCCCAGCATTTCAGGAGGCCATGGCAGGATG NA/A/A/A FALSE TRUE FALSE TRUE . . . . 50 57 1.6848e-06 0.32511 1.42 1.33678 +401 1 22298947 22298947 NA/C/C/NA NA/CAAAAAAAA/CAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 8 . . 0.00000 25.00 0.00000 +402 1 22350322 22350322 NA/NA/A/NA NA/NA/AAC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 24.00 0.00000 +403 1 22411737 22411737 NA/A/A/NA NA/AAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00001 18.00 0.00000 +404 1 22411737 22411737 NA/A/A/NA NA/AAAAAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 6 . . 0.00001 18.00 0.00000 +405 1 22411737 22411737 NA/A/A/NA NA/AAAAAG/AAAG/NA FALSE FALSE TRUE FALSE . . . . 5 . . 0.00001 18.00 0.00000 +406 1 22415050 22415050 A/NA/NA/NA AT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 9.09 . . . . . . +407 1 22415051 22415051 G/NA/NA/NA GGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 9.09 . . . . . . +408 1 22436691 22436692 NA/NA/TA/TA NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 7 1.6452e-01 0.48571 12.00 0.00000 +409 1 22657975 22657976 NA/CA/NA/CA NA/C/NA/C FALSE TRUE FALSE TRUE . . . . 1 15 3.1352e-02 . . . +410 1 22673892 22673895 NA/AAAG/AAAG/AAAG NA/A/A/A FALSE FALSE FALSE TRUE . . . . 3 14 3.9130e-02 1.00000 15.00 0.89263 +411 1 2274296 2274297 NA/AT/NA/AT NA/A/NA/A FALSE FALSE FALSE TRUE . . . . 1 31 7.5783e-04 . . . +412 1 22794581 22794582 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +413 1 22800392 22800392 T/NA/NA/NA TCTTTTCATATTCTAAATAATACTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.94 8.95 . . . . . . +414 1 22904548 22904548 NA/NA/G/NA NA/NA/GCATGTGTGCATGAGTATGTATGCATGTGTGTGCATGTAGCGTCAGTGTATGCATGTGTGCGTGAGTGTATGCATGTGTGCATGTGATGCGTATGTATGCATGCGTGTGCATGTGTGTGACTATGTATGCATGTGTGTATGTATGCGTGTGTGTGCATGTGTGCGTGAGTATGTGCATTGAGTGCATGCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00012 4.00 0.00000 +415 1 22905084 22905084 NA/NA/G/NA NA/NA/GTGTGTGCATGTGTGCATGAGTGTATGTGCAATGTGCGTGTGCATGTGTGTGAGTGTATGCATGTGTGCGTGCACATGTGTGCGAGTGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.05690 1.00 0.00000 +416 1 22944533 22944533 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +417 1 22967697 22967699 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.60 8.84 . . . . . . +418 1 23004825 23004829 NA/NA/NA/ACGTG NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 11 7.3359e-02 . . . +419 1 2302665 2302665 NA/C/C/C NA/CACAACCACA/CACAACCACA/CACAACCACA FALSE FALSE FALSE TRUE . . . . 9 11 7.9421e-02 1.00000 6.00 1.00562 +420 1 23130236 23130238 NA/GTA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 2 . . . . . +421 1 23161118 23161118 NA/C/C/NA NA/CA/CA/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.05183 12.00 0.10271 +422 1 23275378 23275378 T/NA/NA/NA TAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 6.38 . . . . . . +423 1 23275380 23275380 C/NA/NA/NA CCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 6.38 . . . . . . +424 1 2332705 2332706 NA/NA/AC/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.27126 5.00 0.00000 +425 1 23368928 23368928 NA/NA/A/A NA/NA/ATATTATTAT/ATATTATTAT FALSE FALSE FALSE TRUE . . . . . 73 4.0398e-08 0.00000 5.00 0.12740 +426 1 23381505 23381505 G/NA/NA/NA GAATATTTTTTATTATTTATTTATTATATTTAACTTGACTTATAAGAAGATAAACTTGGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 . 11.74 9.28 . . . . . . +427 1 23443935 23443936 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04685 11.00 0.00000 +428 1 23524562 23524563 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +429 1 23562170 23562170 G/NA/NA/NA GGTTTCCTTAGCAATTCTATGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.50 9.21 . . . . . . +430 1 236111 236112 NA/CT/CT/CT NA/C/C/C FALSE TRUE FALSE TRUE . . . . 1 21 6.8801e-03 0.01296 4.00 0.32465 +431 1 23616319 23616320 NA/GA/GA/GA NA/G/G/G FALSE FALSE FALSE TRUE . . . . 1 15 2.5944e-02 0.07065 14.00 0.21132 +432 1 23662609 23662609 NA/C/C/NA NA/CA/CAAAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 28.00 0.00000 +433 1 2367788 2367789 NA/NA/TC/TC NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 21 7.7399e-03 0.09150 3.00 0.00000 +434 1 23702383 23702383 NA/C/C/C NA/CA/CA/CA FALSE FALSE FALSE TRUE . . . . 1 13 4.7431e-02 0.11691 15.00 0.27053 +435 1 23718938 23718942 NA/NA/A/AATAC NA/NA/ATACTCCATACATC/A FALSE FALSE TRUE FALSE . . . . . 0 8.8112e-01 0.00976 2.00 0.00000 +436 1 237528 237529 NA/CA/NA/C NA/CAAAAA/NA/CAAAA FALSE FALSE FALSE TRUE . . . . 4 18 1.5361e-02 . . . +437 1 237528 237529 NA/CA/NA/C NA/C/NA/CAAAA FALSE FALSE FALSE TRUE . . . . 1 18 1.5361e-02 . . . +438 1 23821722 23821722 NA/NA/A/NA NA/NA/AGAGTAACAGGCTTAGGACAATTACGATGTGAGGAGTAATAGGCCTAGGACAATTACGATGTGAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +439 1 23922256 23922260 GCATT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.90 7.63 . . . . . . +440 1 23952454 23952454 NA/NA/G/NA NA/NA/GATAATGATAGGGATGATGGTGATGGTGATGATGATGGTGATGATGGGGATGATGGTGATGGTGATGATGGTGATGTTGATGAATGGTGGTGATGGTGGCAATGTTGGTGATGATGGTAATGATAATGGTGGTGGAGGTGATGATGATGATGATAAGGATGATAATGATGGTGGAGGTGATGATCATGGTAAAGGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00214 2.00 0.00000 +441 1 23952478 23952478 NA/NA/G/NA NA/NA/GCTGATGGTATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02556 2.00 0.00000 +442 1 24030192 24030199 NA/TATATTAC/TATATTAC/NA NA/T/T/NA FALSE TRUE TRUE FALSE . . . . 7 . . 0.08333 3.00 0.00000 +443 1 24072002 24072002 NA/A/NA/A NA/AT/NA/AT FALSE FALSE FALSE TRUE . . . . 1 13 4.6702e-02 . . . +444 1 24159264 24159266 NA/AGT/A/A NA/A/AGTGT/AGTGT FALSE FALSE FALSE TRUE . . . . 2 14 3.7615e-02 0.00326 23.00 0.11919 +445 1 24159264 24159264 NA/A/A/A NA/AGTGT/AGTGT/AGTGT FALSE FALSE FALSE TRUE . . . . 4 14 3.7615e-02 0.00326 23.00 0.11919 +446 1 24159264 24159266 NA/AGT/A/A NA/AGTGT/AGTGT/AGTGT FALSE FALSE FALSE TRUE . . . . 2 14 3.7615e-02 0.00326 23.00 0.11919 +447 1 24173832 24173832 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +448 1 24226300 24226303 NA/CAGA/C/C NA/CAAGA/CAGAAAGAAAGAAAGAAAAGAAAAAAAAGAAAGAAAAGAAAGAAAGAAAGGAAAGAAGGAAAGAAAGAAAGAA/CA FALSE FALSE TRUE FALSE . . . . 1 0 8.1818e-01 0.00014 7.00 0.00000 +449 1 24226300 24226303 NA/CAGA/C/C NA/C/CAGAAAGAAAGAAAGAAAAGAAAAAAAAGAAAGAAAAGAAAGAAAGAAAGGAAAGAAGGAAAGAAAGAAAGAA/CA FALSE FALSE TRUE FALSE . . . . 3 0 8.1818e-01 0.00014 7.00 0.00000 +450 1 24290087 24290087 NA/C/C/NA NA/CAT/CAT/NA FALSE TRUE FALSE FALSE . . . . 2 . . 1.00000 6.00 0.00000 +451 1 24319178 24319179 NA/NA/NA/GC NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 17 1.7534e-02 . . . +452 1 24357747 24357748 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.6374e-01 . . . +453 1 24481706 24481708 ATG/NA/ATG/NA A/NA/A/NA FALSE FALSE TRUE FALSE 60.00 0.000 7.17 4.60 . . . 0.01868 7.00 0.00000 +454 1 24490069 24490072 NA/NA/CTTT/CTTT NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 13 4.8515e-02 0.02017 6.00 0.00000 +455 1 24617119 24617119 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +456 1 24671680 24671681 NA/NA/NA/GC NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 5 2.8571e-01 . . . +457 1 25075718 25075718 NA/T/T/T NA/TA/TA/TA FALSE FALSE FALSE TRUE . . . . 1 14 3.5410e-02 0.01264 15.00 0.09753 +458 1 25091149 25091149 NA/G/NA/NA NA/GA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +459 1 25129202 25129203 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 14 3.8037e-02 . . . +460 1 25322776 25322777 NA/NA/CA/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +461 1 253243 253245 NA/NA/ACT/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01367 4.00 0.00000 +462 1 2540473 2540477 NA/TACAC/NA/TACAC NA/T/NA/T FALSE FALSE FALSE TRUE . . . . 4 3 4.0806e-01 . . . +463 1 25523209 25523209 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +464 1 25613276 25613276 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +465 1 2584644 2584646 ACC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 35.04 -2.399 147.53 34.17 . . . . . . +466 1 2589688 2589688 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 13 4.7679e-02 . . . +467 1 2597367 2597368 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.9804e-01 . . . +468 1 26149013 26149018 NA/NA/NA/CTTTTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 15 2.8215e-02 . . . +469 1 2619639 2619640 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 14 3.7486e-02 . . . +470 1 26204890 26204894 NA/NA/TATAA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.13009 9.00 0.00000 +471 1 26235126 26235135 NA/NA/TATTATTATT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 16.00 0.00000 +472 1 2627109 2627109 C/NA/NA/NA CCTG/NA/NA/NA TRUE FALSE FALSE FALSE 21.73 -1.581 13.20 7.26 . . . . . . +473 1 26455275 26455275 NA/NA/NA/T NA/NA/NA/TCA FALSE FALSE FALSE TRUE . . . . . 45 2.9357e-05 . . . +474 1 26555930 26555930 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 16 2.1834e-02 . . . +475 1 26567735 26567735 NA/NA/A/NA NA/NA/ATTTTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 26.00 0.00000 +476 1 26583087 26583087 NA/NA/T/T NA/NA/TTTTC/TTTTC FALSE FALSE TRUE TRUE . . . . . 12 5.2632e-02 0.04801 4.00 0.00000 +477 1 26711805 26711806 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6023e-02 . . . +478 1 26762892 26762896 TTTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.211 18.32 11.04 . . . . . . +479 1 26765217 26765217 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 9 1.0714e-01 . . . +480 1 26838847 26838847 NA/NA/T/NA NA/NA/TACACACACAAACACACACACACACACACACACACAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 3.00 0.00000 +481 1 2693465 2693466 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 20 9.6796e-03 . . . +482 1 27172802 27172802 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 6 2.4074e-01 . . . +483 1 27222134 27222135 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 13 4.0642e-02 0.01346 12.00 0.06964 +484 1 27224144 27224149 AGGGTG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 24.01 7.83 . . . . . . +485 1 27387962 27387963 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 18 1.3426e-02 0.00194 23.00 0.08389 +486 1 27402731 27402731 NA/NA/C/NA NA/NA/GAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.06179 0.00 0.00000 +487 1 27433686 27433686 NA/NA/C/NA NA/NA/CACACACACACACACCCACACACACCCATCTCCACACATACACACACAGCCCCTCCACACACAAACCCATCTCCAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00056 9.00 0.00000 +488 1 27433722 27433723 NA/NA/AA/NA NA/NA/CCACACACCCACCCAGCCCCTCCACACACACACCCACACCCACACACCCAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00004 0.00 0.00000 +489 1 27471564 27471564 NA/NA/G/G NA/NA/GA/GA FALSE FALSE FALSE TRUE . . . . . 17 1.8258e-02 0.00008 18.00 0.05702 +490 1 27474486 27474487 NA/NA/CA/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01155 11.00 0.00000 +491 1 27580005 27580006 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 7 1.7787e-01 . . . +492 1 27612958 27612959 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.6233e-02 . . . +493 1 27647392 27647393 NA/NA/CT/CT NA/NA/C/C FALSE FALSE TRUE TRUE . . . . . 8 1.5826e-01 0.10122 12.00 0.00000 +494 1 27699264 27699264 NA/NA/A/NA NA/NA/TTTTTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00014 0.00 0.00000 +495 1 27966096 27966098 NA/NA/NA/CTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.8176e-02 . . . +496 1 28002090 28002091 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00930 11.00 0.00000 +497 1 28007364 28007372 NA/NA/CTTTCTTTT/CTTTCTTTT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 46 2.4438e-05 0.00327 27.00 0.22529 +498 1 28194816 28194817 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 19 1.1364e-02 . . . +499 1 28243107 28243107 T/NA/T/NA TTGTGTGTGTGTG/NA/TTGTGTGTGTGTG/NA FALSE FALSE TRUE FALSE 57.63 -0.669 1.80 4.57 . . . 0.00004 25.00 0.00000 +500 1 28257344 28257344 NA/NA/NA/T NA/NA/NA/TTACA FALSE FALSE FALSE TRUE . . . . . 13 4.4118e-02 . . . +501 1 28333848 28333849 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 20 8.0769e-03 . . . +502 1 28534251 28534254 NA/NA/NA/CCAA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 19 1.1811e-02 . . . +503 1 28582245 28582245 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.294 12.04 6.51 . . . . . . +504 1 28595993 28595994 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 14 3.3278e-02 . . . +505 1 28639103 28639105 AAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.35 -6.777 19.85 7.60 . . . . . . +506 1 28684150 28684346 GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAAGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATCTTGCCACTGCACTCCAGCCGGGGCCACAGAGCGAGACTCCGTCTCCAAAAAAAATAAAAAATAAAAATAAATAAAAATAAAAATACAAAAAATTAGCCGGGCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 58.48 -2.472 8.25 7.54 . . . . . . +507 1 28884574 28884575 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 13 4.9439e-02 . . . +508 1 28924881 28924884 CTTA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.09 8.02 . . . . . . +509 1 28962326 28962327 NA/NA/NA/GT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 14 3.2898e-02 . . . +510 1 28998896 28998897 NA/NA/NA/AT NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 7 1.9192e-01 . . . +511 1 2902573 2902573 NA/A/A/A NA/ATCCATCCTCCATCC/ATCCATCCTCCATCC/ATCCATCCTCCATCC FALSE FALSE FALSE TRUE . . . . 14 28 1.5480e-03 0.00208 5.00 0.14182 +512 1 29169478 29169478 NA/NA/NA/G NA/NA/NA/GA FALSE FALSE FALSE TRUE . . . . . 6 2.4074e-01 . . . +513 1 29259017 29259018 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 10 8.7702e-02 . . . +514 1 2937914 2937916 NA/GTC/NA/GTC NA/G/NA/G FALSE TRUE FALSE TRUE . . . . 2 17 1.6968e-02 . . . +515 1 2942459 2942459 NA/NA/G/NA NA/NA/GATGACAGTGATGGTGATGATGGTAATGACAATGATGGTGATGATGATGGTGATGATGGTGATGGTGATGATGATGGTGATGATGGTA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00041 2.00 0.00000 +516 1 2942467 2942467 NA/NA/T/NA NA/NA/TGATGGTGATGATGATGGTAATGACATGGTGGTGTGATCATGATGATGGTGAGGATGGTGGTGGTGATGATGGTAGCTGGTGACGATAATGATGGTGGTGATGATGGTGATGATGACAATGATGGTGATCATGATGGTGATGATGATGGTGATGGC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00013 1.00 0.00000 +517 1 2961928 2961928 G/NA/NA/NA GGATCAAGGAGTCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 12.82 . . . . . . +518 1 2985542 2985543 NA/AG/AG/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 1.00000 11.00 0.00000 +519 1 30651234 30651234 T/NA/NA/NA TTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 6.32 . . . . . . +520 1 3098037 3098052 NA/NA/CGCAGTCTTACACACA/NA NA/NA/TG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01121 3.00 0.00000 +521 1 31411751 31411751 T/NA/NA/NA TAGAC/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 . 13.37 7.88 . . . . . . +522 1 3177306 3177306 NA/NA/A/NA NA/NA/ATGATGTTGGTGATGGTGGTGATGATGATGGCATGATGGCAGTGATTCAAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 3.00 0.00000 +523 1 3187224 3187225 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +524 1 3187225 3187228 NA/NA/AGGA/NA NA/NA/GG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00005 2.00 0.00000 +525 1 3187227 3187228 NA/GA/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +526 1 3236878 3236880 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 21.28 6.59 . . . . . . +527 1 32917655 32917659 GTATT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.87 0.000 18.74 7.35 . . . . . . +528 1 3398879 3398879 NA/G/G/NA NA/GGGGGGGCGGGTAGCC/GGGGGGGCGGGTAGCC/NA FALSE TRUE FALSE FALSE . . . . 15 . . 1.00000 7.00 0.00000 +529 1 3403148 3403148 A/NA/NA/NA AGAGTTAACTACAAACAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.31 6.33 . . . . . . +530 1 3500398 3500434 NA/NA/GCAGCCACCAGACAACCCGCAGCCACCAGACAACGCG/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . 0.12253 2.00 0.00000 +531 1 3500449 3500449 NA/C/C/NA NA/CGCACAGCCACCAGACAAT/CGCACAGCCACCAGACAAT/NA FALSE FALSE TRUE FALSE . . . . 18 . . 0.00000 1.00 0.00000 +532 1 35008216 35008216 A/NA/NA/NA ACTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.75 12.06 . . . . . . +533 1 3504600 3504623 NA/NA/CCAGGAGGGGGCAGGACAGGGCAG/NA NA/NA/ATAGGAGGAGATAGGAGGGGACAGGAGTGGACAGAAGGAGACAGGAGGGGACAGGAGTGGACAGGAGACAGGAGGGGACAGGAATGGCCAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00699 0.00 0.00000 +534 1 35731970 35731973 AAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.07 11.068 27.24 6.94 . . . . . . +535 1 36026087 36026092 CCTGCT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.75 8.63 . . . . . . +536 1 3610560 3610560 NA/NA/C/C NA/NA/CT/CT FALSE FALSE FALSE TRUE . . . . . 4 3.3766e-01 0.50000 4.00 0.00000 +537 1 3645570 3645572 NA/NA/NA/GAC NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 26 2.2668e-03 . . . +538 1 36624636 36624640 GTTAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.95 0.324 12.85 14.19 . . . . . . +539 1 37262884 37262886 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.37 12.36 . . . . . . +540 1 3738791 3738810 NA/NA/GACTGACAGACAGACAGAGG/NA NA/NA/CC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 6.00 0.00000 +541 1 3771434 3771434 NA/A/A/A NA/ATT/ATT/ATT FALSE FALSE FALSE TRUE . . . . 2 20 8.5769e-03 0.00948 21.00 0.31697 +542 1 3771434 3771434 NA/A/A/A NA/AT/ATT/ATT FALSE FALSE FALSE TRUE . . . . 1 20 8.5769e-03 0.00948 21.00 0.31697 +543 1 3785163 3785163 NA/NA/A/NA NA/NA/ACCACACCATACCAGACCACACCACACCAGGCCACACCACACCAAGCCACAACCACGCCACACCACACCAGG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +544 1 37917967 37917967 G/NA/NA/NA GAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 34.93 7.49 . . . . . . +545 1 37917968 37917968 T/NA/NA/NA TTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 34.94 7.24 . . . . . . +546 1 3801133 3801134 NA/NA/AT/AT NA/NA/A/A FALSE FALSE TRUE TRUE . . . . . 14 3.2147e-02 0.02997 11.00 0.00000 +547 1 3816054 3816074 NA/CCAGACACTGGCACCCCCCTT/CCAGACACTGGCACCCCCCTT/CCAGACACTGGCACCCCCCTT NA/C/C/C FALSE FALSE FALSE TRUE . . . . 20 30 9.0133e-04 0.02310 2.00 2.17313 +548 1 3825025 3825025 NA/NA/T/NA NA/NA/TCTCACA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00006 21.00 0.00000 +549 1 39487 39487 NA/NA/NA/A NA/NA/NA/AC FALSE FALSE FALSE TRUE . . . . . 24 3.7652e-03 . . . +550 1 39790775 39790775 T/NA/NA/NA TAAGTTTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.81 19.73 . . . . . . +551 1 40279122 40279124 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.31 0.271 9.93 6.93 . . . . . . +552 1 40803798 40803798 A/NA/NA/NA AAAATGCATGTACCACAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 19.26 6.32 . . . . . . +553 1 41069654 41069656 TGA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.12 12.95 . . . . . . +554 1 41091997 41091999 TAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.07 15.18 . . . . . . +555 1 4110792 4110793 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +556 1 4127223 4127223 NA/NA/NA/T NA/NA/NA/TCATG FALSE FALSE FALSE TRUE . . . . . 4 3.5478e-01 . . . +557 1 41599553 41599553 T/NA/NA/NA TAGATTTTCTA/NA/NA/NA TRUE FALSE FALSE FALSE 59.67 -4.282 9.91 9.41 . . . . . . +558 1 4363250 4363294 NA/NA/CTCCACCCGACCCCACCCCACCCCACCCCACCCCACCCCACCCCA/NA NA/NA/ATAAATTCCTTTCGAGAGCATTCAATTTAGATGCATTCCATTCGAGTCCATTCCATTCTATTCCATTCCATTTCATTCCATTCAATTCCATTCATATCCACTCGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +559 1 43801445 43801445 G/NA/NA/NA GCATATATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.11 6.37 . . . . . . +560 1 44170440 44170442 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.08 3.841 7.46 6.30 . . . . . . +561 1 44643868 44643868 A/NA/NA/NA AATTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.44 9.05 . . . . . . +562 1 44925096 44925096 C/NA/NA/NA CTTATTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.73 6.59 . . . . . . +563 1 45456018 45456018 T/NA/NA/NA TAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.56 9.36 . . . . . . +564 1 4603741 4603741 NA/NA/C/NA NA/NA/CTATCTATCTATCTATCTATCTCTCTATCTATCTATCTATCTTATCTATTTATCTATCTATCTATCATCTACCTATCTCTCTGTCATCTATCTATCTCTCTGCCTTTGTGTCTATCTACCTATCTCTATCATCTATCTAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +565 1 4820251 4820253 CTG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.37 -0.494 5.58 6.50 . . . . . . +566 1 4827659 4827697 NA/NA/TTATCATCATCACCATCTTTATCATTACCATCATCACCA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00230 2.00 0.00000 +567 1 48649644 48649644 T/NA/NA/NA TAAAGCATAGCAAGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.85 15.84 . . . . . . +568 1 49106010 49106010 T/NA/NA/NA TA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.57 . . . . . . +569 1 4931550 4931552 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 -0.201 22.99 6.94 . . . . . . +570 1 4942374 4942375 NA/AT/AT/NA NA/A/A/NA FALSE TRUE TRUE FALSE . . . . 1 . . 0.02211 12.00 0.00000 +571 1 4948380 4948380 NA/NA/C/NA NA/NA/CAAAAAAAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 18.00 0.00000 +572 1 49555455 49555457 GAC/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.88 6.54 . . . . . . +573 1 49862038 49862040 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.21 8.15 . . . . . . +574 1 4999496 4999496 NA/NA/G/NA NA/NA/GTCTCTCCATATGACGTCAGTGTCCTCCATATGACATCAATATCCTCCATATGATGTCAATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 1.00 0.00000 +575 1 49997601 49997601 C/NA/NA/NA CAACAGTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.60 8.94 . . . . . . +576 1 50089515 50089515 A/NA/NA/NA ATTTAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 8.87 . . . . . . +577 1 50241552 50241552 T/NA/NA/NA TTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 11.88 . . . . . . +578 1 50289048 50289048 T/NA/NA/NA TAAATTGATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.44 16.95 . . . . . . +579 1 50289049 50289049 C/NA/NA/NA CATACGGTTGATTTGTATGTGTATAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.39 16.95 . . . . . . +580 1 5084764 5084764 NA/NA/A/NA NA/NA/AAAATAAATAAATAAAT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00734 12.00 0.00000 +581 1 51049318 51049318 C/NA/NA/NA CAGTGAAACA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 9.13 . . . . . . +582 1 51067364 51067366 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.02 3.388 16.53 11.51 . . . . . . +583 1 51146696 51146699 GAAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 12.26 . . . . . . +584 1 51177132 51177132 T/NA/NA/NA TAGATCGGAAGAGCGTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.68 7.31 . . . . . . +585 1 51640089 51640089 G/NA/NA/NA GATGGTATTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.23 6.43 . . . . . . +586 1 51690830 51690830 C/NA/NA/NA CAAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.36 9.27 . . . . . . +587 1 5180539 5180539 NA/NA/C/NA NA/NA/AAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +588 1 51844686 51844686 C/NA/NA/NA CTTTGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.48 9.18 . . . . . . +589 1 51844688 51844688 T/NA/NA/NA TTTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.18 . . . . . . +590 1 52434901 52434901 C/NA/NA/NA CAAGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.60 9.63 . . . . . . +591 1 52468797 52468799 TTA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.95 6.95 . . . . . . +592 1 52535438 52535438 T/NA/NA/NA TCATATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.49 13.23 . . . . . . +593 1 5325296 5325297 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 9 1.1565e-01 . . . +594 1 53485886 53485886 G/NA/NA/NA GTTGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.66 8.94 . . . . . . +595 1 540710 540712 CGA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 51.65 -1.451 13.57 13.14 . . . . . . +596 1 547113 547115 NA/NA/NA/GGT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 22 5.2405e-03 . . . +597 1 547217 547219 NA/NA/NA/GGT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 13 4.8200e-02 . . . +598 1 5498907 5498910 NA/NA/NA/CTTA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 17 1.5850e-02 . . . +599 1 55983974 55983984 ATCCATCCATC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.62 0.000 11.36 8.91 . . . . . . +600 1 5609675 5609675 C/NA/NA/NA CCCACCG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.55 9.22 . . . . . . +601 1 56362200 56362203 AGCC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.84 19.33 . . . . . . +602 1 56513091 56513091 A/NA/NA/NA AACTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.37 . . . . . . +603 1 56513093 56513097 CATCA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.94 9.24 . . . . . . +604 1 5664508 5664508 NA/NA/C/NA NA/NA/CTCTCTCTCTCTCATCTCTGTCTTTCTCTCTCTCTCTCATCTCTCTCCCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00032 14.00 0.00000 +605 1 57581791 57581791 G/NA/NA/NA GCTTCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 6.32 . . . . . . +606 1 5810611 5810615 TTGTC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.12 7.536 15.85 13.42 . . . . . . +607 1 58262211 58262214 GATA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.000 19.27 10.63 . . . . . . +608 1 5855966 5855983 NA/ACCAGTACTCAGTCACCG/ACCAGTACTCAGTCACCG/ACCAGTACTCAGTCACCG NA/A/A/A FALSE FALSE FALSE TRUE . . . . 17 14 3.5344e-02 0.00000 1.00 0.00000 +609 1 5872338 5872339 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 9 1.2468e-01 . . . +610 1 58794335 58794335 T/NA/NA/NA TAACGCTGTGGTTGTAGTATTTCCAAGC/NA/NA/NA TRUE FALSE FALSE FALSE 59.83 0.000 23.61 7.89 . . . . . . +611 1 5881482 5881482 NA/NA/G/NA NA/NA/GGAAGGAAGGAAAGAGAGAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 10.00 0.00000 +612 1 58938598 58938598 G/NA/NA/NA GAGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.60 6.82 . . . . . . +613 1 59008389 59008389 G/NA/NA/NA GTATTTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.18 4.398 9.96 9.46 . . . . . . +614 1 59726039 59726040 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 3.61 6.49 . . . . . . +615 1 59726041 59726048 TGTGTGTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.17 6.49 . . . . . . +616 1 5973211 5973212 NA/CA/NA/CA NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 18 1.4590e-02 . . . +617 1 5986573 5986573 C/NA/NA/NA CA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 27.39 8.05 . . . . . . +618 1 5992132 5992133 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 10 9.3583e-02 . . . +619 1 60264195 60264195 T/NA/NA/NA TGAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.56 9.05 . . . . . . +620 1 6065211 6065212 NA/NA/AC/NA NA/NA/TT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.51471 1.00 0.00000 +621 1 6065447 6065447 NA/NA/NA/G NA/NA/NA/GT FALSE FALSE FALSE TRUE . . . . . 7 1.9231e-01 . . . +622 1 6065495 6065495 NA/NA/G/NA NA/NA/GAGCTGAGTGGGGTGACGTGGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00023 3.00 0.00000 +623 1 6065981 6065982 NA/NA/NA/TC NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 10 9.4721e-02 . . . +624 1 6066218 6066219 NA/NA/TC/TC NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 5 2.5926e-01 0.53770 6.00 0.00000 +625 1 61356823 61356825 GGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.09 6.71 . . . . . . +626 1 6148763 6148766 NA/AAAT/AAAT/AAAT NA/A/A/A FALSE FALSE FALSE TRUE . . . . 3 14 3.5721e-02 0.02445 9.00 0.14871 +627 1 61631966 61631966 A/NA/NA/NA AAGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.58 12.82 . . . . . . +628 1 61631967 61631967 T/NA/NA/NA TGTCTAAGCA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.58 12.82 . . . . . . +629 1 63013003 63013003 A/NA/NA/NA AGAGTACAGCAAAGTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.15 9.11 . . . . . . +630 1 63117847 63117850 TCCC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.34 12.35 . . . . . . +631 1 6332302 6332306 GATGA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 23.18 7.59 . . . . . . +632 1 6366267 6366267 NA/NA/A/A NA/NA/AGAGGGG/AGAGGGG FALSE FALSE FALSE TRUE . . . . . 4 3.2353e-01 0.65289 5.00 1.76791 +633 1 63986883 63986883 A/NA/NA/NA ATTTGTAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.10 9.69 . . . . . . +634 1 6417930 6417930 NA/C/NA/C NA/CTT/NA/CTT FALSE FALSE FALSE TRUE . . . . 2 14 3.9629e-02 . . . +635 1 65018790 65018790 G/NA/NA/NA GTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.25 15.79 . . . . . . +636 1 65190377 65190377 A/NA/NA/NA AG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.65 8.94 . . . . . . +637 1 65190379 65190379 T/NA/NA/NA TGC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.66 8.94 . . . . . . +638 1 6530965 6530965 NA/C/C/NA NA/CG/CG/NA FALSE TRUE FALSE FALSE . . . . 1 . . 1.00000 4.00 0.00000 +639 1 6541922 6541923 NA/TA/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +640 1 65523704 65523704 T/NA/NA/NA TTTACATGAAAATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.63 8.90 . . . . . . +641 1 6582943 6582943 NA/C/C/NA NA/CAA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 2 . . 0.00000 0.00 0.00000 +642 1 6582943 6582943 NA/C/C/NA NA/CA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 1 . . 0.00000 0.00 0.00000 +643 1 6582943 6582943 NA/C/C/NA NA/CAAA/AAAAAAA/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 0.00 0.00000 +644 1 6583221 6583221 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 24 3.7764e-03 . . . +645 1 66451871 66451878 CACAATGT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.74 9.33 . . . . . . +646 1 6660077 6660079 AAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.46 6.97 . . . . . . +647 1 6666725 6666726 NA/NA/NA/CA NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 5 2.8571e-01 . . . +648 1 6724301 6724302 NA/CT/NA/CT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 18 1.4821e-02 . . . +649 1 6734787 6734787 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +650 1 67359685 67359685 A/NA/NA/NA AGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 12.82 . . . . . . +651 1 67576182 67576182 A/NA/NA/NA AACAGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.54 12.70 . . . . . . +652 1 6777615 6777615 A/NA/NA/NA ATTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.96 9.46 . . . . . . +653 1 68212752 68212752 A/NA/NA/NA ATAATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 8.77 . . . . . . +654 1 68393888 68393888 C/NA/NA/NA CATTAAAAAAAGATATGCAGCCAGGCGCAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.59 6.55 . . . . . . +655 1 6894212 6894212 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 6 2.2973e-01 . . . +656 1 69009958 69009958 T/NA/NA/NA TGG/NA/NA/NA TRUE FALSE FALSE FALSE 59.70 -4.827 7.53 10.45 . . . . . . +657 1 69192187 69192187 T/NA/NA/NA TGATTTAAGTAAAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.85 9.69 . . . . . . +658 1 693620 693621 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 49.88 -2.429 10.18 6.56 . . . . . . +659 1 69725408 69725408 A/NA/NA/NA AAAAATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.37 8.91 . . . . . . +660 1 69725409 69725409 C/NA/NA/NA CT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 8.91 . . . . . . +661 1 6997794 6997796 NA/NA/AGT/NA NA/NA/CATCATTCTCACTACCAC/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00879 0.00 0.00000 +662 1 7000990 7000991 NA/NA/AA/NA NA/NA/GGGGGGTCCTCAGAGGGAGAGGGATCCTCCCGGGGAAGGGGGATCCTCACGGGGAAGGGCATCCTCAGGGGGAAG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +663 1 70015621 70015621 A/NA/NA/NA ACATAAATTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.99 12.02 . . . . . . +664 1 70040383 70040383 C/NA/NA/NA CTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 22.88 16.48 . . . . . . +665 1 70040384 70040384 A/NA/NA/NA ATCTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 22.88 16.47 . . . . . . +666 1 70070001 70070001 T/NA/NA/NA TAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.95 12.65 . . . . . . +667 1 7007607 7007608 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +668 1 7044150 7044150 NA/NA/G/NA NA/NA/ATGAATGGATGGTTGGGTGGATGGATGGGTTGGATGAGTGAACCGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00522 0.00 0.00000 +669 1 70766861 70766863 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.61 7.90 . . . . . . +670 1 71104257 71104257 C/NA/NA/NA CTAGCTGTACATTAGA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.64 6.38 . . . . . . +671 1 71787025 71787025 A/NA/NA/NA AGTGCTTGATAT/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.282 10.27 9.02 . . . . . . +672 1 7216335 7216336 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +673 1 7226868 7226868 NA/G/NA/NA NA/GT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +674 1 72340027 72340027 A/NA/NA/NA AATC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 17.76 8.98 . . . . . . +675 1 72602225 72602225 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.37 . . . . . . +676 1 72602226 72602226 A/NA/NA/NA AACAATAATAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.45 9.37 . . . . . . +677 1 72657998 72657998 G/NA/NA/NA GATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.65 13.39 . . . . . . +678 1 72799605 72799605 A/NA/NA/NA AATAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.42 9.90 . . . . . . +679 1 72930915 72930915 A/NA/NA/NA AGAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.52 . . . . . . +680 1 7370802 7370802 NA/NA/C/C NA/NA/TT/CTTTTT FALSE FALSE FALSE TRUE . . . . . 4 3.4737e-01 1.00000 0.00 1.34324 +681 1 74138051 74138051 T/NA/NA/NA TATATATATA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.68 13.08 . . . . . . +682 1 74538174 74538176 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.31 4.939 5.18 7.18 . . . . . . +683 1 74663493 74663493 G/NA/NA/NA GTTTTTTTGGGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.09 6.65 . . . . . . +684 1 7489683 7489683 NA/NA/G/NA NA/NA/GTGATAATGATGATGATGGTGATGACAGTGCTGATAATAGATCATAATGGTGATGATGATGATGGTGATTATTGTAATAGTGATGACAGTGATGATGATAATGATGGTGATAAGAGTGGATAATGATAATAACACTAATGGTGATGATGATAATGATGGTGGTATGATGATGTGGATGGTAATGGTGATGATAACAGTGGATAATGATGGCAATGCAAGTGA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +685 1 74987200 74987202 GTA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.30 -0.322 8.20 6.50 . . . . . . +686 1 7506241 7506242 NA/GA/NA/GA NA/G/NA/G FALSE FALSE FALSE TRUE . . . . 1 13 4.3944e-02 . . . +687 1 75275380 75275380 T/NA/NA/NA TATAATTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 9.26 . . . . . . +688 1 7540316 7540316 NA/T/T/T NA/TGTGTGA/TGTGTGA/TGTGTGA FALSE FALSE FALSE TRUE . . . . 6 51 7.8435e-06 1.00000 3.00 0.90209 +689 1 7662140 7662140 NA/NA/NA/T NA/NA/NA/TTTCC FALSE FALSE FALSE TRUE . . . . . 5 2.6815e-01 . . . +690 1 76986983 76986985 TAC/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.17 4.398 10.49 7.19 . . . . . . +691 1 77032198 77032206 CTCTTTCTT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.62 13.56 . . . . . . +692 1 77354419 77354419 A/NA/NA/NA ATAGGAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.93 9.57 . . . . . . +693 1 77367889 77367889 T/NA/NA/NA TATCATGTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 9.17 . . . . . . +694 1 7762392 7762396 AAAAC/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.34 6.73 . . . . . . +695 1 77712396 77712396 T/NA/NA/NA TCCC/NA/NA/NA TRUE FALSE FALSE FALSE 59.47 -6.890 9.30 13.86 . . . . . . +696 1 7825019 7825020 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +697 1 78854924 78854924 A/NA/NA/NA AATGATGGT/NA/NA/NA TRUE FALSE FALSE FALSE 54.76 -2.406 4.52 6.92 . . . . . . +698 1 79475391 79475391 T/NA/NA/NA TTTG/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 . 7.29 7.80 . . . . . . +699 1 79615102 79615102 T/NA/NA/NA TGATTGTCCC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.37 8.94 . . . . . . +700 1 79879535 79879535 A/NA/NA/NA AGCCATGGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.87 9.75 . . . . . . +701 1 80078641 80078641 T/NA/NA/NA TTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.24 13.38 . . . . . . +702 1 80209962 80209962 T/NA/NA/NA TAACA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.49 16.40 . . . . . . +703 1 80229884 80229886 TCA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.04 8.47 . . . . . . +704 1 8041720 8041721 NA/GT/NA/G NA/GTTT/NA/GTT FALSE FALSE FALSE TRUE . . . . 2 13 4.8663e-02 . . . +705 1 8041720 8041721 NA/GT/NA/G NA/G/NA/GTT FALSE FALSE FALSE TRUE . . . . 1 13 4.8663e-02 . . . +706 1 80557556 80557556 A/NA/NA/NA ATATAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.87 8.91 . . . . . . +707 1 8087009 8087009 NA/NA/A/NA NA/NA/AGGGACAGTGAGAGTGAGGGACAGTGTAGGACAGTGAGGGACAGTGT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 2.00 0.00000 +708 1 8117228 8117229 NA/NA/CT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.02760 11.00 0.00000 +709 1 81654021 81654022 CA/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.70 26.96 . . . . . . +710 1 81685072 81685072 T/NA/NA/NA TTTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.45 8.87 . . . . . . +711 1 81927897 81927897 G/NA/NA/NA GC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.37 10.45 . . . . . . +712 1 81927899 81927899 A/NA/NA/NA ATTCTTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.36 10.45 . . . . . . +713 1 820722 820724 NA/NA/NA/GCT NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . 14 3.4521e-02 . . . +714 1 820723 820733 NA/NA/CTATCCTTAAC/NA NA/NA/AACCTTATCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00362 2.00 0.00000 +715 1 820733 820733 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 12 5.2656e-02 . . . +716 1 820749 820749 NA/NA/C/NA NA/NA/CT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00903 6.00 0.00000 +717 1 8212709 8212709 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +718 1 8217903 8217940 NA/NA/TGGAAGAGGAGGAGGAAGAAGAAGGAGAAGAAGGAAGA/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01367 2.00 0.00000 +719 1 825392 825449 NA/NA/CTATTTTTTCTTTTGTTGGGGGGGTGGGGAGGTGGATGGAGTCTCACTCTGTCACCCG/NA NA/NA/TCTTTTTTTTTTTGCTGGGGGTGGGGTGTGGTGGATGGAATCTTGCTCTGATGCCCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00408 6.00 0.00000 +720 1 82571241 82571241 G/NA/NA/NA GGGAGAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.36 12.71 . . . . . . +721 1 82571243 82571243 A/NA/NA/NA ATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 18.36 12.71 . . . . . . +722 1 8276437 8276438 NA/NA/CT/CT NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . 13 4.1046e-02 0.18148 11.00 0.39278 +723 1 82979355 82979355 T/NA/NA/NA TGACATAAACAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.46 12.87 . . . . . . +724 1 83044829 83044834 ATGGGG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.82 9.83 . . . . . . +725 1 8321412 8321442 NA/TCTTTCTTTCCTTCCTTCCTTCCTTCCTTCC/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 30 . . . . . +726 1 83215295 83215295 A/NA/NA/NA ATC/NA/NA/NA TRUE FALSE FALSE FALSE 59.75 0.000 12.38 8.81 . . . . . . +727 1 83215297 83215297 A/NA/NA/NA AAAGAATAGTAT/NA/NA/NA TRUE FALSE FALSE FALSE 59.74 0.000 12.38 8.81 . . . . . . +728 1 8328298 8328300 NA/CT/NA/CTT NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 1 11 7.2188e-02 . . . +729 1 83332 83332 NA/NA/G/G NA/NA/GA/GA FALSE FALSE TRUE FALSE . . . . . 4 3.5296e-01 0.11415 3.00 0.00000 +730 1 83571902 83571905 TTAA/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.61 7.61 . . . . . . +731 1 8361340 8361368 NA/TGGGATTCATCAATATCCTGTAGCTGGGC/TGGGATTCATCAATATCCTGTAGCTGGGC/TGGGATTCATCAATATCCTGTAGCTGGGC NA/T/T/T FALSE FALSE FALSE TRUE . . . . 28 44 3.6744e-05 0.00000 1.00 0.02225 +732 1 83903033 83903034 TG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 54.28 -2.659 12.94 7.14 . . . . . . +733 1 8404939 8404939 NA/C/C/C NA/CACAT/CACAT/CACAT FALSE FALSE FALSE TRUE . . . . 4 13 4.4272e-02 0.10205 11.00 0.50232 +734 1 8427001 8427002 NA/NA/NA/AC NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . 9 1.1103e-01 . . . +735 1 85297559 85297561 CAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.91 7.08 . . . . . . +736 1 85992513 85992513 A/NA/NA/NA AC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 24.04 8.07 . . . . . . +737 1 86005852 86005852 G/NA/NA/NA GTGGGCTCAATAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.77 9.09 . . . . . . +738 1 86005854 86005854 G/NA/NA/NA GT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 9.09 . . . . . . +739 1 86190136 86190142 AGTAGCT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.39 8.50 . . . . . . +740 1 86229006 86229011 CACAAG/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.60 10.34 . . . . . . +741 1 86247418 86247418 A/NA/NA/NA AGATTATT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.33 12.22 . . . . . . +742 1 8624885 8624885 A/A/A/NA ATATGTGTGTGTGTG/ATATGTGTGTGTGTG/ATATGTGTGTGTGTG/NA FALSE FALSE TRUE FALSE 54.85 . 1.55 4.44 14 . . 0.00940 8.00 0.00000 +743 1 86285375 86285375 G/NA/NA/NA GATTCATA/NA/NA/NA TRUE FALSE FALSE FALSE 59.63 0.000 7.55 12.60 . . . . . . +744 1 86383049 86383049 C/NA/NA/NA CAGTATTGGTCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.26 9.62 . . . . . . +745 1 8655217 8655218 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +746 1 8661076 8661076 NA/C/NA/C NA/CTTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 3 13 4.5516e-02 . . . +747 1 8661076 8661076 NA/C/NA/C NA/CTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 2 13 4.5516e-02 . . . +748 1 8661076 8661076 NA/C/NA/C NA/CTTTT/NA/CTTT FALSE FALSE FALSE TRUE . . . . 4 13 4.5516e-02 . . . +749 1 8696001 8696011 NA/NA/TTTATTTTATC/TTTATTTTATC NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . 15 2.9557e-02 0.21037 6.00 1.99060 +750 1 87347091 87347091 T/NA/NA/NA TTTTATTAAGTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.37 9.09 . . . . . . +751 1 8738547 8738548 NA/CA/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +752 1 87663930 87663932 ATG/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.71 6.75 . . . . . . +753 1 87863468 87863468 A/NA/NA/NA ATCCCTGTCCCACACCAAGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.08 . . . . . . +754 1 87863470 87863470 C/NA/NA/NA CGCCCCATCCCCTGTGTCTCACCTTTGGCTCCCCCTGGGCTTCT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 5.72 9.13 . . . . . . +755 1 8818914 8818914 NA/NA/NA/C NA/NA/NA/CA FALSE FALSE FALSE TRUE . . . . . 9 1.1210e-01 . . . +756 1 89108561 89108570 TTTGTTGTTG/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 4.75 10.26 . . . . . . +757 1 89205442 89205442 T/NA/NA/NA TCTAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 16.27 8.94 . . . . . . +758 1 89298924 89298924 C/NA/NA/NA CTGAAAAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.02 9.46 . . . . . . +759 1 89310538 89310542 CAAAT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.000 25.75 7.48 . . . . . . +760 1 8980238 8980239 NA/CT/NA/NA NA/C/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +761 1 90026153 90026167 ATCTCATTGTTCAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 44.89 -1.614 3.58 6.74 . . . . . . +762 1 90228194 90228196 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 25.53 7.10 . . . . . . +763 1 9038731 9038731 NA/A/A/NA NA/AAAC/AAAAC/NA FALSE FALSE TRUE FALSE . . . . 3 . . 0.00000 38.00 0.00000 +764 1 9038731 9038731 NA/A/A/NA NA/AAAAC/AAAAC/NA FALSE FALSE TRUE FALSE . . . . 4 . . 0.00000 38.00 0.00000 +765 1 90845810 90845812 GCA/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.11 6.73 . . . . . . +766 1 9102468 9102470 ATG/NA/NA/ATG A/NA/NA/A FALSE FALSE FALSE TRUE 60.00 0.000 11.43 5.83 . 11 7.3657e-02 . . . +767 1 91092921 91092925 GTTAT/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 19.85 7.67 . . . . . . +768 1 91134042 91134043 CT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.42 3.170 11.13 47.36 . . . . . . +769 1 9119186 9119190 NA/NA/CCTTT/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . 0.01332 3.00 0.00000 +770 1 91194750 91194750 G/NA/NA/NA GAACAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.88 13.23 . . . . . . +771 1 91194752 91194752 G/NA/NA/NA GTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.88 13.23 . . . . . . +772 1 91669881 91669893 AAAATAAATAAAT/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.03 0.228 12.69 7.77 . . . . . . +773 1 919994 919998 A/A/ATTTA/NA ATTTCTTTCTTTC/ATTTCTTTCTTTCTTTCTTTCTTTC/TATTTCTTTCTTTCTTTCTTTCTTTCTTCC/NA FALSE FALSE TRUE FALSE 60.88 . 1.01 13.86 24 . . 0.00000 11.00 0.00000 +774 1 922666 922666 NA/C/C/C NA/CTTTTT/CTTTTTTT/CTTTT FALSE FALSE TRUE FALSE . . . . 5 0 9.1950e-01 0.00000 23.00 0.00000 +775 1 922666 922666 NA/C/C/C NA/CTTTT/CTTTTTTT/CTTTT FALSE FALSE TRUE FALSE . . . . 4 0 9.1950e-01 0.00000 23.00 0.00000 +776 1 92743421 92743421 C/NA/NA/NA CATGACCTCTCCCTTTGCTTAAAGAAAAGCTGTAAG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.94 6.35 . . . . . . +777 1 92891010 92891010 T/NA/NA/NA TG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.20 13.38 . . . . . . +778 1 93223310 93223310 T/NA/NA/NA TAAAACTCAAAACTG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.88 13.65 . . . . . . +779 1 9385283 9385289 NA/NA/CACCCCC/NA NA/NA/TACCA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 13.00 0.00000 +780 1 9385284 9385286 NA/ACC/NA/ACC NA/A/NA/A FALSE FALSE FALSE TRUE . . . . 2 50 9.2329e-06 . . . +781 1 9416962 9416962 NA/NA/G/NA NA/NA/AGATGAGTGAATAATGGATGGATA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00000 0.00 0.00000 +782 1 9439843 9439848 NA/GAAAGA/GA/NA NA/G/G/NA FALSE FALSE TRUE FALSE . . . . 5 . . 0.00377 4.00 0.00000 +783 1 94824 94826 NA/NA/NA/CTT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 10 9.3883e-02 . . . +784 1 951440 951441 NA/NA/NA/CT NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . 12 5.6683e-02 . . . +785 1 9550378 9550378 NA/C/NA/NA NA/CA/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +786 1 95572410 95572410 C/NA/NA/NA CCAATTTTTGGT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.50 8.87 . . . . . . +787 1 9559353 9559354 NA/AT/AT/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 1 . . 0.17512 11.00 0.24393 +788 1 96177553 96177553 G/NA/NA/NA GGATAAATATTCTTTTGCAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.52 9.01 . . . . . . +789 1 96185056 96185056 T/NA/NA/NA TCTAA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.15 8.71 . . . . . . +790 1 96384544 96384544 C/NA/NA/NA CTGG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.35 9.46 . . . . . . +791 1 964745 964745 NA/NA/A/NA NA/NA/ATCTATGCAGGCAGGTAGGGGGATCAGTG/NA FALSE FALSE TRUE FALSE . . . . . . . 0.04384 1.00 0.00000 +792 1 9684705 9684705 NA/C/C/C NA/CTTT/CTTTTT/CTT FALSE FALSE TRUE FALSE . . . . 3 2 5.2930e-01 0.00000 24.00 0.00000 +793 1 9684705 9684705 NA/C/C/C NA/CTT/CTTTTT/CTT FALSE FALSE TRUE FALSE . . . . 2 2 5.2930e-01 0.00000 24.00 0.00000 +794 1 97132272 97132272 T/NA/NA/NA TAATCATATACATCTAGTATG/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.80 8.66 . . . . . . +795 1 97167512 97167512 A/NA/NA/NA ATTTCTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.05 9.13 . . . . . . +796 1 97234858 97234858 A/NA/NA/NA AGCAGTCAGAAC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.66 9.46 . . . . . . +797 1 97238365 97238365 A/NA/NA/NA AGAATAGGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.87 9.88 . . . . . . +798 1 97348958 97348962 CTATT/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.10 10.000 23.43 10.26 . . . . . . +799 1 9740505 9740505 NA/NA/NA/T NA/NA/NA/TA FALSE FALSE FALSE TRUE . . . . . 8 1.5766e-01 . . . +800 1 9744960 9744960 NA/C/NA/NA NA/CT/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +801 1 97456393 97456393 A/NA/NA/NA AACTACATAAT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.46 9.21 . . . . . . +802 1 9771638 9771639 NA/AT/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 1 . . . . . +803 1 9810773 9810773 NA/NA/C/NA NA/NA/AAAAAAAAA/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00008 0.00 0.00000 +804 1 98413333 98413333 A/NA/NA/NA AACATTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.29 8.71 . . . . . . +805 1 98660552 98660552 G/NA/NA/NA GTA/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.64 9.46 . . . . . . +806 1 99224314 99224314 G/NA/NA/NA GATATATAATAATAATAGCCTCTC/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 8.60 . . . . . . +807 1 99248350 99248350 A/NA/NA/NA ATTTTAGTTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.84 9.36 . . . . . . +808 1 9995188 9995189 NA/NA/NA/TA NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . 9 1.1105e-01 . . . +809 1 99968642 99968642 G/NA/NA/NA GGTT/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.76 8.44 . . . . . . +810 1 9999600 9999600 NA/NA/C/NA NA/NA/CTTTT/NA FALSE FALSE TRUE FALSE . . . . . . . 0.00002 25.00 0.00000 diff --git a/test/results/indel-predicted.txt b/test/results/indel-predicted.txt index ae458af..007da8c 100644 --- a/test/results/indel-predicted.txt +++ b/test/results/indel-predicted.txt @@ -1,2 +1,2 @@ -X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs TRUTH_confidence -1 1 17820432 17820433 AT/AT/AT/AT A/A/A/A 0.571875 +Chr START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs SMuRF_score +1 1 17820432 17820433 AT/AT/AT/AT A/A/A/A 0.6210418 diff --git a/test/results/indel-stats.txt b/test/results/indel-stats.txt index 2717cd7..5ea2bc7 100644 --- a/test/results/indel-stats.txt +++ b/test/results/indel-stats.txt @@ -2,9 +2,9 @@ Passed_Calls Mutect2 383 FreeBayes 85 VarDict 166 -VarScan 158 -Atleast1 765 -Atleast2 25 +VarScan 208 +Atleast1 810 +Atleast2 30 Atleast3 2 All4 0 -Model 1 +SMuRF_INDEL 1 diff --git a/test/results/snv-parse.txt b/test/results/snv-parse.txt index 01b375c..6c090d4 100644 --- a/test/results/snv-parse.txt +++ b/test/results/snv-parse.txt @@ -1,5685 +1,5701 @@ -X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs FILTER_Mutect2 FILTER_Freebayes FILTER_Vardict FILTER_Varscan m2_MQ m2_MQRankSum m2_TLOD f_MQM f_MQMR f_ODDS vs_SSC vs_SPV vd_SSF vd_SOR -1 1 100006410 100006410 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.65 . . . . . . . -2 1 100060264 100060264 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.67 . . . . . . . -3 1 100080141 100080141 T/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 14.73 . . . . . . . -4 1 100092090 100092090 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.21 . . . . . . . -5 1 100134429 100134429 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.71 . . . . . . . -6 1 100152081 100152081 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.92 . . . . . . . -7 1 100174506 100174506 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.70 . . . . . . . -8 1 100209733 100209733 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.94 . . . . . . . -9 1 100225346 100225346 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.82 . . . . . . . -10 1 10022874 10022874 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.922 7.12 . . . . . . . -11 1 100250155 100250155 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.83 . . . . . . . -12 1 100258580 100258580 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.47 . . . . . . . -13 1 100296768 100296768 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.01 . . . . . . . -14 1 100297044 100297044 T/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.31 . . . . . . . -15 1 100297045 100297045 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.31 . . . . . . . -16 1 10033850 10033850 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.16 . . . . . . . -17 1 100358950 100358950 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.50 . . . . . . . -18 1 100383278 100383278 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.53 . . . . . . . -19 1 100418794 100418794 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.96 . . . . . . . -20 1 100444255 100444255 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.03 . . . . . . . -21 1 100470006 100470006 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.81 . . . . . . . -22 1 100473149 100473149 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.99 . . . . . . . -23 1 10047524 10047524 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.32 . . . . . . . -24 1 100479215 100479215 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.17 . . . . . . . -25 1 100494646 100494646 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.37 . . . . . . . -26 1 100497166 100497166 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.58 . . . . . . . -27 1 10055061 10055061 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.239 10.93 . . . . . . . -28 1 100577886 100577886 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.90 . . . . . . . -29 1 100578957 100578957 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.528 7.05 . . . . . . . -30 1 10058291 10058291 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.51 . . . . . . . -31 1 100655405 100655405 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.45 . . . . . . . -32 1 100721127 100721127 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.77 . . . . . . . -33 1 100734295 100734295 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.21 . . . . . . . -34 1 100808158 100808158 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.95 . . . . . . . -35 1 100860521 100860521 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.15 . . . . . . . -36 1 100892324 100892324 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.79 . . . . . . . -37 1 100899307 100899307 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -38 1 100900987 100900987 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.25 . . . . . . . -39 1 10093338 10093338 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.79 . . . . . . . -40 1 100985990 100985990 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.22 . . . . . . . -41 1 100997475 100997475 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.01 . . . . . . . -42 1 10103045 10103045 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 9 1.1102e-01 . . -43 1 101046707 101046707 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.56 . . . . . . . -44 1 101077751 101077751 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.14 . . . . . . . -45 1 1011858 1011858 NA/T/T/NA NA/C/C/NA . TRUE FALSE FALSE FALSE . . 40.0000 0.0000 7.377760 . . 1.00000 0.00000 -46 1 101200921 101200921 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 12.09 . . . . . . . -47 1 101286523 101286523 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.96 . . . . . . . -48 1 101314659 101314659 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.40 . . . . . . . -49 1 101327940 101327940 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.66 . . . . . . . -50 1 101341644 101341644 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.10 . . . . . . . -51 1 1013597 1013597 NA/NA/NA/T NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 4 3.6774e-01 . . -52 1 101386497 101386497 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.06 . . . . . . . -53 1 101388692 101388692 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.821 6.92 . . . . . . . -54 1 101447189 101447189 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.54 . . . . . . . -55 1 1014491 1014491 NA/NA/NA/A NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 10 9.0194e-02 . . -56 1 10145409 10145409 G/NA/G/NA T/NA/T/NA PASS FALSE FALSE FALSE FALSE 0.000 12.50 . . . . . 0.07507 0.00000 -57 1 101474973 101474973 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.41 . . . . . . . -58 1 101478368 101478368 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.20 . . . . . . . -59 1 10148579 10148579 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.05 . . . . . . . -60 1 10151604 10151604 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.86 . . . . . . . -61 1 101521146 101521146 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.37 . . . . . . . -62 1 101577254 101577254 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.27 . . . . . . . -63 1 101594262 101594262 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.41 . . . . . . . -64 1 101614905 101614905 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.65 . . . . . . . -65 1 101648707 101648707 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.31 . . . . . . . -66 1 101660179 101660179 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.29 . . . . . . . -67 1 101686 101686 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 10 8.1600e-02 . . -68 1 101737832 101737832 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.869 6.40 . . . . . . . -69 1 101792161 101792161 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.07 . . . . . . . -70 1 101839305 101839305 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.54 . . . . . . . -71 1 1018394 1018394 NA/NA/NA/T NA/NA/NA/G . 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FALSE FALSE TRUE FALSE . . . . . 4 3.2164e-01 . . -89 1 102498496 102498496 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.88 . . . . . . . -90 1 10254507 10254507 NA/A/A/A NA/T/T/T . 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FALSE FALSE TRUE FALSE . . . . . 4 3.5897e-01 0.01791 0.12587 -1874 1 167566155 167566155 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.81 . . . . . . . -1875 1 16757064 16757064 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.63 . . . . . . . -1876 1 167607430 167607430 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.39 . . . . . . . -1877 1 167633674 167633674 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.72 . . . . . . . -1878 1 167739740 167739740 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.06 . . . . . . . -1879 1 167777424 167777424 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.39 . . . . . . . -1880 1 167796739 167796739 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.12 . . . . . . . -1881 1 167882550 167882550 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.55 . . . . . . . -1882 1 1678846 1678846 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.042 7.13 . . . . . . . -1883 1 167890579 167890579 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.27 . . . . . . . -1884 1 167992322 167992322 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.47 . . . . . . . -1885 1 167998641 167998641 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.07 . . . . . . . -1886 1 168052849 168052849 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.76 . . . . . . . -1887 1 168065991 168065991 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.96 . . . . . . . -1888 1 168102599 168102599 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.52 . . . . . . . -1889 1 16818039 16818039 NA/NA/NA/T NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 7 1.8357e-01 . . -1890 1 168227529 168227529 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.41 . . . . . . . -1891 1 168232625 168232625 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.68 . . . . . . . -1892 1 16831510 16831510 NA/A/A/NA NA/G/G/NA . TRUE FALSE FALSE FALSE . . 37.3636 58.4103 16.686500 . . 0.01186 0.13061 -1893 1 16831572 16831572 NA/C/NA/NA NA/T/NA/NA . TRUE FALSE FALSE FALSE . . . . . . . . . -1894 1 16831573 16831573 NA/T/NA/NA NA/G/NA/NA . TRUE FALSE FALSE FALSE . . . . . . . . . -1895 1 16831583 16831583 NA/G/G/NA NA/A/A/NA . TRUE FALSE FALSE FALSE . . 29.8462 59.5077 5.952830 . . 0.05234 0.25995 -1896 1 168317293 168317293 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.239 6.61 . . . . . . . -1897 1 168337681 168337681 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.45 . . . . . . . -1898 1 16834012 16834012 NA/NA/A/A NA/NA/T/T . FALSE TRUE TRUE FALSE . . . . . 23 4.6169e-03 0.01680 0.00000 -1899 1 16835584 16835584 A/A/NA/NA G/G/NA/NA PASS FALSE FALSE FALSE FALSE -5.497 10.55 . . . . . . . -1900 1 16836026 16836026 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.020 9.45 . . . . . . . -1901 1 16837823 16837823 NA/G/G/G NA/A/A/A . FALSE FALSE TRUE FALSE . . 29.6875 31.2302 2.685460 14 3.5817e-02 0.04186 0.30755 -1902 1 16838071 16838071 C/NA/C/NA T/NA/T/NA PASS FALSE FALSE FALSE FALSE -0.443 41.58 . . . . . 0.16951 0.55827 -1903 1 16839489 16839489 A/NA/A/NA G/NA/G/NA PASS FALSE FALSE FALSE FALSE -1.855 6.39 . . . . . 0.56896 0.71438 -1904 1 16840226 16840226 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -5.254 22.28 . . . . . . . -1905 1 168407223 168407223 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.13 . . . . . . . -1906 1 16841381 16841381 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.980 7.28 . . . . . . . -1907 1 16841952 16841952 NA/G/G/G NA/A/A/A . TRUE FALSE TRUE FALSE . . 33.6364 26.5233 2.696670 14 3.7240e-02 0.10805 0.30053 -1908 1 168422263 168422263 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.57 . . . . . . . -1909 1 168422408 168422408 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.94 . . . . . . . -1910 1 16842968 16842968 NA/NA/C/C NA/NA/T/T . FALSE FALSE TRUE FALSE . . . . . 16 2.0327e-02 0.06641 0.44358 -1911 1 168509047 168509047 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.08 . . . . . . . -1912 1 168531443 168531443 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 22.39 . . . . . . . -1913 1 16855554 16855554 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 8 1.4084e-01 . . -1914 1 16858329 16858329 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 13 4.4944e-02 . . -1915 1 168613652 168613652 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.65 . . . . . . . -1916 1 16861614 16861614 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.468 10.87 . . . . . . . -1917 1 16862261 16862261 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -3.176 15.15 . . . . . . . -1918 1 168624937 168624937 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.18 . . . . . . . -1919 1 16863201 16863201 C/NA/NA/C T/NA/NA/T . FALSE FALSE TRUE FALSE -4.235 5.84 . . . 26 2.1013e-03 . . -1920 1 168635009 168635009 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.59 . . . . . . . -1921 1 168637825 168637825 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.49 . . . . . . . -1922 1 168648467 168648467 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.856 8.80 . . . . . . . -1923 1 168650656 168650656 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.54 . . . . . . . -1924 1 168698460 168698460 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -1925 1 168702579 168702579 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.65 . . . . . . . -1926 1 16870422 16870422 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.053 6.71 . . . . . . . -1927 1 16870947 16870947 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.393 13.55 . . . . . . . -1928 1 168713570 168713570 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.34 . . . . . . . -1929 1 168716055 168716055 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.485 12.47 . . . . . . . -1930 1 168726766 168726766 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.18 . . . . . . . -1931 1 16874041 16874041 NA/C/C/NA NA/G/G/NA . TRUE FALSE FALSE FALSE . . 36.0909 36.7222 2.834750 . . 0.01245 0.09484 -1932 1 16876705 16876705 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.571 11.91 . . . . . . . -1933 1 16877844 16877844 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 15 3.1241e-02 . . -1934 1 16885297 16885297 NA/C/C/C NA/A/A/A . FALSE FALSE TRUE FALSE . . 49.1923 52.0895 16.829200 13 4.1865e-02 0.20034 0.54408 -1935 1 16887040 16887040 NA/A/A/A NA/G/G/G . TRUE FALSE TRUE FALSE . . 59.6897 58.2463 31.785600 22 5.5592e-03 0.00947 0.31653 -1936 1 168871799 168871799 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.69 . . . . . . . -1937 1 16890681 16890681 C/NA/C/NA G/NA/G/NA PASS FALSE FALSE FALSE FALSE -2.632 21.29 . . . . . 0.29443 0.50855 -1938 1 168908031 168908031 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.60 . . . . . . . -1939 1 16891870 16891870 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.920 7.07 . . . . . . . -1940 1 168931014 168931014 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.34 . . . . . . . -1941 1 16894763 16894763 G/NA/NA/G A/NA/NA/A . FALSE FALSE TRUE FALSE -4.938 21.61 . . . 14 3.5690e-02 . . -1942 1 16897721 16897721 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.419 7.29 . . . . . . . -1943 1 16900847 16900847 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.081 6.85 . . . . . . . -1944 1 16901303 16901303 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.631 6.83 . . . . . . . -1945 1 169029402 169029402 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.83 . . . . . . . -1946 1 169034384 169034384 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.15 . . . . . . . -1947 1 169036458 169036458 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.34 . . . . . . . -1948 1 16903798 16903798 T/NA/NA/T C/NA/NA/C . FALSE FALSE TRUE FALSE -4.074 27.10 . . . 15 2.5155e-02 . . -1949 1 16903803 16903803 T/NA/NA/T C/NA/NA/C . FALSE FALSE TRUE FALSE -3.780 26.90 . . . 13 4.2013e-02 . . -1950 1 16905492 16905492 T/NA/T/NA C/NA/C/NA PASS FALSE FALSE FALSE FALSE -2.169 13.09 . . . . . 0.41052 0.60775 -1951 1 16905788 16905788 A/NA/NA/A G/NA/NA/G . FALSE FALSE TRUE FALSE -2.716 15.23 . . . 13 4.2483e-02 . . -1952 1 16905789 16905789 T/NA/NA/T C/NA/NA/C . FALSE FALSE TRUE FALSE -2.733 15.23 . . . 14 3.5945e-02 . . -1953 1 16905800 16905800 G/NA/NA/G A/NA/NA/A . FALSE FALSE TRUE FALSE -2.320 13.09 . . . 14 3.4880e-02 . . -1954 1 16907164 16907164 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.594 19.23 . . . . . . . -1955 1 16907970 16907970 C/NA/NA/C A/NA/NA/A . FALSE FALSE TRUE FALSE 0.329 22.11 . . . 21 7.3898e-03 . . -1956 1 16908793 16908793 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.219 9.08 . . . . . . . -1957 1 16911937 16911937 C/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.856 9.05 . . . . . . . -1958 1 169121682 169121682 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.75 . . . . . . . -1959 1 169123087 169123087 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.11 . . . . . . . -1960 1 16915243 16915243 NA/NA/A/A NA/NA/G/G . FALSE FALSE TRUE FALSE . . . . . 18 1.5580e-02 0.19910 0.42065 -1961 1 169168864 169168864 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.35 . . . . . . . -1962 1 169175169 169175169 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.30 . . . . . . . -1963 1 16918895 16918895 NA/C/C/C NA/T/T/T . FALSE FALSE TRUE FALSE . . 39.7143 41.0062 29.180800 25 2.7198e-03 0.01140 0.33988 -1964 1 16919665 16919665 NA/T/T/T NA/C/C/C . FALSE FALSE TRUE FALSE . . 58.5111 58.2184 9.311190 13 4.5978e-02 0.10075 0.57925 -1965 1 169209502 169209502 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.57 . . . . . . . -1966 1 169215195 169215195 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.71 . . . . . . . -1967 1 16921601 16921601 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.028 7.39 . . . . . . . -1968 1 16922230 16922230 NA/G/G/G NA/C/C/C . FALSE FALSE TRUE FALSE . . . . . 14 3.1661e-02 0.69088 0.80297 -1969 1 169226138 169226138 T/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -5.124 11.18 . . . . . . . -1970 1 169226327 169226327 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.842 7.46 . . . . . . . -1971 1 16923291 16923291 A/A/A/A G/G/G/G . FALSE FALSE TRUE FALSE -2.945 79.39 39.5952 44.1358 30.894500 21 6.3558e-03 0.00601 0.37886 -1972 1 16923517 16923517 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.651 18.90 . . . . . . . -1973 1 169248290 169248290 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.207 7.44 . . . . . . . -1974 1 169260225 169260225 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.255 7.78 . . . . . . . -1975 1 169274196 169274196 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.71 . . . . . . . -1976 1 16928862 16928862 NA/T/T/T NA/C/C/C . FALSE FALSE TRUE FALSE . . 58.9459 59.2951 15.203900 20 9.2028e-03 0.01133 0.39835 -1977 1 16931453 16931453 NA/T/T/T NA/C/C/C . FALSE FALSE TRUE FALSE . . 60.0000 58.5485 10.421800 15 3.0773e-02 0.03502 0.46184 -1978 1 16932859 16932859 A/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.258 27.45 . . . . . . . -1979 1 16935677 16935677 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.85 . . . . . . . -1980 1 16936759 16936759 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.53 . . . . . . . -1981 1 169372065 169372065 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.008 11.38 . . . . . . . -1982 1 169374673 169374673 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.01 . . . . . . . -1983 1 16938426 16938426 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.01 . . . . . . . -1984 1 169412406 169412406 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.97 . . . . . . . -1985 1 16942588 16942588 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 11.03 . . . . . . . -1986 1 16945570 16945570 A/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.078 39.50 . . . . . . . -1987 1 169464427 169464427 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.09 . . . . . . . -1988 1 169485819 169485819 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.92 . . . . . . . -1989 1 16952764 16952764 A/NA/A/NA C/NA/C/NA PASS FALSE FALSE FALSE FALSE 0.000 24.51 . . . . . 0.75631 0.88123 -1990 1 169553094 169553094 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.19 . . . . . . . -1991 1 169566207 169566207 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.35 . . . . . . . -1992 1 16957963 16957963 G/G/G/G A/A/A/A PASS FALSE FALSE FALSE FALSE -1.821 24.43 59.9722 59.8366 9.877510 3 4.6977e-01 1.00000 1.06558 -1993 1 16958063 16958063 C/C/NA/NA T/T/NA/NA PASS FALSE FALSE FALSE FALSE 1.058 34.07 . . . . . . . -1994 1 169630082 169630082 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.397 7.51 . . . . . . . -1995 1 16970822 16970822 C/C/C/C A/A/A/A . FALSE FALSE TRUE FALSE 0.924 98.92 59.1286 59.4047 1.072100 14 3.9392e-02 0.30341 0.75272 -1996 1 169730364 169730364 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.13 . . . . . . . -1997 1 16974592 16974592 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 7 1.9212e-01 . . -1998 1 16975082 16975082 A/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.085 14.12 . . . . . . . -1999 1 169755504 169755504 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.20 . . . . . . . -2000 1 16976436 16976436 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.164 10.46 . . . . . . . -2001 1 169765647 169765647 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.45 . . . . . . . -2002 1 169766146 169766146 T/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.12 . . . . . . . -2003 1 16977426 16977426 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.749 6.40 . . . . . . . -2004 1 16979538 16979538 A/NA/NA/A T/NA/NA/T . FALSE FALSE TRUE FALSE -1.793 5.31 . . . 15 2.7607e-02 . . -2005 1 16980198 16980198 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.730 8.08 . . . . . . . -2006 1 16982110 16982110 NA/G/G/G NA/A/A/A . TRUE FALSE FALSE FALSE . . 27.0000 0.0000 8.070910 0 8.4732e-01 1.00000 0.00000 -2007 1 169833926 169833926 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.87 . . . . . . . -2008 1 16983551 16983551 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 5 2.7143e-01 . . -2009 1 169854004 169854004 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.66 . . . . . . . -2010 1 16988492 16988492 NA/NA/G/NA NA/NA/T/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.23077 0.00000 -2011 1 16988627 16988627 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 15 3.0672e-02 . . -2012 1 169920180 169920180 A/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.14 . . . . . . . -2013 1 169920181 169920181 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.14 . . . . . . . -2014 1 169938635 169938635 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.27 . . . . . . . -2015 1 169942068 169942068 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.04 . . . . . . . -2016 1 169977319 169977319 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.84 . . . . . . . -2017 1 169999107 169999107 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.29 . . . . . . . -2018 1 17000346 17000346 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 13 4.1253e-02 . . -2019 1 170010186 170010186 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.88 . . . . . . . -2020 1 17001480 17001480 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.515 7.51 . . . . . . . -2021 1 17002002 17002002 NA/NA/C/C NA/NA/G/G . 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FALSE FALSE TRUE FALSE . . . . . 3 4.5833e-01 . . -2812 1 25353235 25353235 NA/T/T/T NA/A/A/A . FALSE TRUE FALSE FALSE . . 60.0000 60.0000 85.415700 0 1.0000e+00 0.00000 0.00000 -2813 1 25380177 25380177 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.45 . . . . . . . -2814 1 25393944 25393944 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.28 . . . . . . . -2815 1 25405764 25405764 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.51 . . . . . . . -2816 1 25406224 25406224 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.270 8.89 . . . . . . . -2817 1 25426358 25426358 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.27 . . . . . . . -2818 1 25428507 25428507 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.60 . . . . . . . -2819 1 25441835 25441835 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.34 . . . . . . . -2820 1 25449498 25449498 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.09 . . . . . . . -2821 1 254728 254728 NA/NA/T/T NA/NA/G/G . FALSE TRUE FALSE FALSE . . . . . 8 1.3823e-01 0.02232 0.00000 -2822 1 25475191 25475191 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.62 . . . . . . . -2823 1 25482689 25482689 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.93 . . . . . . . -2824 1 25511225 25511225 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.140 6.69 . . . . . . . -2825 1 255185 255185 G/NA/G/G A/NA/A/A . FALSE FALSE TRUE FALSE -1.464 5.92 . . . 14 3.6232e-02 0.18600 0.21196 -2826 1 25542041 25542041 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.38 . . . . . . . -2827 1 25543390 25543390 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.00 . . . . . . . -2828 1 255593 255593 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 21 7.5805e-03 . . -2829 1 25573061 25573061 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.36 . . . . . . . -2830 1 255897 255897 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 11 7.6276e-02 . . -2831 1 25638219 25638219 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -1.915 6.93 . . . . . . . -2832 1 25648090 25648090 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.90 . . . . . . . -2833 1 2569600 2569600 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.55 . . . . . . . -2834 1 25696816 25696816 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.356 7.42 . . . . . . . -2835 1 25725136 25725136 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.183 6.32 . . . . . . . -2836 1 25741764 25741764 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.632 6.85 . . . . . . . -2837 1 25837445 25837445 NA/NA/A/NA NA/NA/G/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.06591 0.00000 -2838 1 25837785 25837785 NA/NA/A/NA NA/NA/T/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.23404 0.00000 -2839 1 25837821 25837821 NA/NA/C/NA NA/NA/T/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.10694 0.00000 -2840 1 2583802 2583802 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 48 1.2738e-05 . . -2841 1 2583829 2583829 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 82 5.8125e-09 . . -2842 1 2585364 2585364 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 13 4.1068e-02 . . -2843 1 25855031 25855031 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.33 . . . . . . . -2844 1 2585751 2585751 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 14 3.4903e-02 . . -2845 1 2585991 2585991 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 35 2.9900e-04 . . -2846 1 25860532 25860532 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.68 . . . . . . . -2847 1 2586067 2586067 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 33 4.1375e-04 . . -2848 1 25863189 25863189 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 12.02 . . . . . . . -2849 1 2586374 2586374 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 2.767 9.19 . . . . . . . -2850 1 2586414 2586414 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 71 6.4674e-08 . . -2851 1 25866594 25866594 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.29 . . . . . . . -2852 1 2586860 2586860 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 37 1.8622e-04 . . -2853 1 2586913 2586913 T/NA/NA/T G/NA/NA/G PASS FALSE FALSE FALSE FALSE -0.473 15.00 . . . 1 7.9206e-01 . . -2854 1 2586947 2586947 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 1.299 8.79 . . . . . . . -2855 1 2587086 2587086 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 32 5.9203e-04 . . -2856 1 2587371 2587371 C/NA/NA/C T/NA/NA/T . FALSE FALSE TRUE FALSE -7.151 36.06 . . . 61 7.1461e-07 . . -2857 1 2587407 2587407 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 42 5.6934e-05 . . -2858 1 2587408 2587408 C/NA/NA/C T/NA/NA/A . FALSE FALSE TRUE FALSE -1.287 4.84 . . . 34 3.8986e-04 . . -2859 1 2587996 2587996 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 7 1.5909e-01 . . -2860 1 2588607 2588607 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 14 3.7232e-02 . . -2861 1 25888735 25888735 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.36 . . . . . . . -2862 1 2589814 2589814 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 13 4.8627e-02 . . -2863 1 2589830 2589830 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 15 3.1275e-02 . . -2864 1 25904275 25904275 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.64 . . . . . . . -2865 1 2590948 2590948 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 15 2.5857e-02 . . -2866 1 2590988 2590988 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 19 1.1974e-02 . . -2867 1 2591273 2591273 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 15 2.7431e-02 . . -2868 1 2591363 2591363 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 14 3.9135e-02 . . -2869 1 2591422 2591422 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 25 2.8419e-03 . . -2870 1 2591603 2591603 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 5 2.7027e-01 . . -2871 1 2591606 2591606 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 8 1.3514e-01 . . -2872 1 2591607 2591607 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 5 2.8529e-01 . . -2873 1 2591739 2591739 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 26 2.4809e-03 . . -2874 1 25919113 25919113 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.248 7.13 . . . . . . . -2875 1 2592314 2592314 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 15 3.0535e-02 . . -2876 1 2592394 2592394 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 13 4.4736e-02 . . -2877 1 25927191 25927191 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.30 . . . . . . . -2878 1 2593541 2593541 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 15 3.0813e-02 . . -2879 1 2594234 2594234 NA/NA/NA/A NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 20 9.5297e-03 . . -2880 1 25952357 25952357 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.95 . . . . . . . -2881 1 25957178 25957178 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.00 . . . . . . . -2882 1 25981440 25981440 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.214 11.42 . . . . . . . -2883 1 2600562 2600562 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 24 3.3747e-03 . . -2884 1 26031728 26031728 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -2885 1 2603318 2603318 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -6.089 44.55 . . . . . . . -2886 1 26043096 26043096 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.41 . . . . . . . -2887 1 26066386 26066386 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.50 . . . . . . . -2888 1 2606687 2606687 NA/NA/NA/T NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 17 1.8155e-02 . . -2889 1 26067946 26067946 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.83 . . . . . . . -2890 1 2606994 2606994 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -3.995 7.31 . . . . . . . -2891 1 2607101 2607101 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 19 1.0217e-02 . . -2892 1 2607399 2607399 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 18 1.5482e-02 . . -2893 1 2607404 2607404 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 14 3.4181e-02 . . -2894 1 2607406 2607406 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 24 3.8020e-03 . . -2895 1 2607415 2607415 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 15 3.1381e-02 . . -2896 1 2609077 2609077 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 21 7.9373e-03 . . -2897 1 2609185 2609185 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 13 4.1666e-02 . . -2898 1 26096281 26096281 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.40 . . . . . . . -2899 1 26112928 26112928 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.81 . . . . . . . -2900 1 2611617 2611617 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 18 1.3135e-02 . . -2901 1 2611620 2611620 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 14 3.3706e-02 . . -2902 1 2611640 2611640 NA/NA/NA/T NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 22 5.5874e-03 . . -2903 1 26116680 26116680 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.49 . . . . . . . -2904 1 2611808 2611808 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 13 4.7029e-02 . . -2905 1 2614235 2614235 NA/NA/NA/G NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 14 3.8932e-02 . . -2906 1 2614428 2614428 NA/NA/NA/A NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 14 3.7440e-02 . . -2907 1 2615474 2615474 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 14 3.4217e-02 . . -2908 1 2615635 2615635 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 13 4.6403e-02 . . -2909 1 2615995 2615995 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -3.820 6.78 . . . . . . . -2910 1 26164548 26164548 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.189 7.09 . . . . . . . -2911 1 2616707 2616707 G/NA/NA/G A/NA/NA/A PASS FALSE FALSE FALSE FALSE -0.060 11.37 . . . 4 3.3972e-01 . . -2912 1 26168907 26168907 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.72 . . . . . . . -2913 1 2617274 2617274 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 14 3.5469e-02 . . -2914 1 2617353 2617353 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 13 4.5382e-02 . . -2915 1 2617373 2617373 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 17 1.8894e-02 . . -2916 1 2617382 2617382 NA/NA/NA/G NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 38 1.3651e-04 . . -2917 1 2617436 2617436 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.713 32.74 . . . . . . . -2918 1 2617672 2617672 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 13 4.7108e-02 . . -2919 1 2618229 2618229 NA/NA/NA/T NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 15 2.5747e-02 . . -2920 1 2618269 2618269 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 21 7.0034e-03 . . -2921 1 2618438 2618438 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 18 1.3950e-02 . . -2922 1 2618492 2618492 T/NA/NA/T A/NA/NA/A PASS FALSE FALSE FALSE FALSE -2.247 37.77 . . . 40 9.7074e-05 . . -2923 1 26186009 26186009 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.03 . . . . . . . -2924 1 2618834 2618834 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 28 1.2874e-03 . . -2925 1 26189429 26189429 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.69 . . . . . . . -2926 1 2619596 2619596 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 20 9.6328e-03 . . -2927 1 2619614 2619614 C/NA/NA/C T/NA/NA/T . FALSE FALSE TRUE FALSE -2.760 22.22 . . . 28 1.4849e-03 . . -2928 1 2619622 2619622 G/NA/NA/G T/NA/NA/T . FALSE FALSE TRUE FALSE -3.060 18.40 . . . 18 1.3000e-02 . . -2929 1 26198633 26198633 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.38 . . . . . . . -2930 1 2620447 2620447 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 13 4.7337e-02 . . -2931 1 26209387 26209387 NA/NA/NA/G NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 12 5.8140e-02 . . -2932 1 2621498 2621498 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 39 1.1363e-04 . . -2933 1 2621688 2621688 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 25 2.6908e-03 . . -2934 1 2622110 2622110 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 14 3.6165e-02 . . -2935 1 2622170 2622170 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 31 7.3970e-04 . . -2936 1 2622177 2622177 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 33 4.6814e-04 . . -2937 1 2622179 2622179 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 26 2.1809e-03 . . -2938 1 26221876 26221876 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.51 . . . . . . . -2939 1 2622211 2622211 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 23 4.2612e-03 . . -2940 1 2622398 2622398 C/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.404 10.90 . . . . . . . -2941 1 2622836 2622836 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 24 3.7411e-03 . . -2942 1 26228559 26228559 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.64 . . . . . . . -2943 1 2622877 2622877 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 17 1.6866e-02 . . -2944 1 2622907 2622907 T/NA/NA/T G/NA/NA/G PASS FALSE FALSE TRUE FALSE -10.119 25.20 . . . 20 8.9132e-03 . . -2945 1 2622939 2622939 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 14 3.8508e-02 . . -2946 1 2623503 2623503 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -3.003 30.36 . . . . . . . -2947 1 2623545 2623545 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 18 1.5151e-02 . . -2948 1 2624174 2624174 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 15 2.6762e-02 . . -2949 1 2624696 2624696 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 22 5.9460e-03 . . -2950 1 2624975 2624975 G/NA/NA/G A/NA/NA/A PASS FALSE FALSE FALSE FALSE -0.568 9.73 . . . 16 2.3090e-02 . . -2951 1 2625036 2625036 NA/NA/NA/A NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 15 2.8618e-02 . . -2952 1 2625267 2625267 C/NA/NA/C G/NA/NA/A PASS FALSE FALSE FALSE FALSE -1.908 20.06 . . . 11 6.7283e-02 . . -2953 1 2625719 2625719 NA/NA/NA/G NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 23 4.4154e-03 . . -2954 1 2625729 2625729 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 30 8.3435e-04 . . -2955 1 26261899 26261899 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.02 . . . . . . . -2956 1 2626292 2626292 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -3.018 8.99 . . . . . . . -2957 1 2626535 2626535 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 18 1.4486e-02 . . -2958 1 2626684 2626684 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 20 8.7926e-03 . . -2959 1 2627358 2627358 NA/NA/NA/C NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 15 2.6815e-02 . . -2960 1 2627368 2627368 T/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.280 13.63 . . . . . . . -2961 1 2627894 2627894 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 14 3.8579e-02 . . -2962 1 2628253 2628253 T/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -0.018 10.42 . . . . . . . -2963 1 2628558 2628558 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.316 26.21 . . . . . . . -2964 1 2628602 2628602 A/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.187 25.88 . . . . . . . -2965 1 2628703 2628703 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 18 1.5313e-02 . . -2966 1 2628781 2628781 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 23 4.9136e-03 . . -2967 1 2628785 2628785 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 37 1.9576e-04 . . -2968 1 2629540 2629540 NA/NA/NA/C NA/NA/NA/T . FALSE FALSE TRUE FALSE . . . . . 25 2.5834e-03 . . -2969 1 26365692 26365692 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.88 . . . . . . . -2970 1 26379647 26379647 NA/NA/C/NA NA/NA/A/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.01069 0.00000 -2971 1 26427394 26427394 NA/NA/NA/T NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 11 7.5188e-02 . . -2972 1 26497159 26497159 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.07 . . . . . . . -2973 1 26546770 26546770 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.77 . . . . . . . -2974 1 26562252 26562252 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.181 7.02 . . . . . . . -2975 1 26591688 26591688 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.77 . . . . . . . -2976 1 26628161 26628161 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 10.75 . . . . . . . -2977 1 26631837 26631837 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.98 . . . . . . . -2978 1 26668339 26668339 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.98 . . . . . . . -2979 1 26668600 26668600 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.57 . . . . . . . -2980 1 26691533 26691533 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.89 . . . . . . . -2981 1 26720690 26720690 NA/NA/NA/C NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 7 1.6585e-01 . . -2982 1 26792973 26792973 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.60 . . . . . . . -2983 1 26842132 26842132 NA/NA/C/NA NA/NA/A/NA . FALSE TRUE FALSE FALSE . . . . . . . 0.00023 0.00000 -2984 1 26846194 26846194 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.61 . . . . . . . -2985 1 2685688 2685688 NA/NA/NA/G NA/NA/NA/A . FALSE FALSE TRUE FALSE . . . . . 18 1.4860e-02 . . -2986 1 26863914 26863914 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.71 . . . . . . . -2987 1 26867784 26867784 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 7 1.6256e-01 . . -2988 1 26871612 26871612 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.31 . . . . . . . -2989 1 2688011 2688011 NA/NA/NA/T NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 18 1.2812e-02 . . -2990 1 2689711 2689711 NA/NA/NA/G NA/NA/NA/A . 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FALSE FALSE TRUE FALSE . . . . . 11 7.5188e-02 . . -5634 1 98598355 98598355 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -5635 1 98599804 98599804 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.05 . . . . . . . -5636 1 98618373 98618373 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.93 . . . . . . . -5637 1 98619399 98619399 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.047 7.36 . . . . . . . -5638 1 98620378 98620378 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.45 . . . . . . . -5639 1 98632380 98632380 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE -2.611 9.14 . . . . . . . -5640 1 98660550 98660550 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.46 . . . . . . . -5641 1 9879741 9879741 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.07 . . . . . . . -5642 1 98833555 98833555 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.37 . . . . . . . -5643 1 98839389 98839389 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.76 . . . . . . . -5644 1 988589 988589 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.43 . . . . . . . -5645 1 98887732 98887732 T/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.38 . . . . . . . -5646 1 98901222 98901222 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.79 . . . . . . . -5647 1 98922909 98922909 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.02 . . . . . . . -5648 1 9892447 9892447 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.293 7.67 . . . . . . . -5649 1 98955927 98955927 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -5650 1 9901778 9901778 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.62 . . . . . . . -5651 1 99078743 99078743 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE -6.625 8.60 . . . . . . . -5652 1 99110323 99110323 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.39 . . . . . . . -5653 1 99122432 99122432 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.248 7.03 . . . . . . . -5654 1 9915195 9915195 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.44 . . . . . . . -5655 1 991740 991740 NA/NA/NA/T NA/NA/NA/G . FALSE FALSE TRUE FALSE . . . . . 3 4.8718e-01 . . -5656 1 9919213 9919213 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.82 . . . . . . . -5657 1 99197309 99197309 A/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.24 . . . . . . . -5658 1 99200411 99200411 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.17 . . . . . . . -5659 1 99211202 99211202 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 12.51 . . . . . . . -5660 1 9923608 9923608 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.25 . . . . . . . -5661 1 99243125 99243125 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.24 . . . . . . . -5662 1 99248349 99248349 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.36 . . . . . . . -5663 1 9926261 9926261 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.31 . . . . . . . -5664 1 99283498 99283498 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.50 . . . . . . . -5665 1 9930056 9930056 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.47 . . . . . . . -5666 1 99346747 99346747 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.282 8.28 . . . . . . . -5667 1 9935359 9935359 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.65 . . . . . . . -5668 1 99366649 99366649 G/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.21 . . . . . . . -5669 1 9944161 9944161 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.53 . . . . . . . -5670 1 9945523 9945523 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 9.96 . . . . . . . -5671 1 99466079 99466079 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 7.43 . . . . . . . -5672 1 99645342 99645342 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.68 . . . . . . . -5673 1 99699311 99699311 T/NA/NA/NA G/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.56 . . . . . . . -5674 1 9971265 9971265 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.40 . . . . . . . -5675 1 99715853 99715853 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.51 . . . . . . . -5676 1 99759054 99759054 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 12.16 . . . . . . . -5677 1 99773620 99773620 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.42 . . . . . . . -5678 1 99844197 99844197 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 6.62 . . . . . . . -5679 1 99864301 99864301 C/NA/NA/NA A/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.14 . . . . . . . -5680 1 9987947 9987947 G/G/G/G C/C/C/C PASS TRUE TRUE FALSE FALSE 0.000 10.36 60.0000 58.8140 24.547800 24 3.6125e-03 0.00401 0.00000 -5681 1 99880333 99880333 G/NA/NA/NA C/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 12.03 . . . . . . . -5682 1 99924239 99924239 G/NA/NA/NA T/NA/NA/NA PASS FALSE FALSE FALSE FALSE 0.000 8.85 . . . . . . . -5683 1 9993308 9993308 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 4 3.4476e-01 . . -5684 1 9993311 9993311 NA/NA/NA/A NA/NA/NA/C . FALSE FALSE TRUE FALSE . . . . . 6 2.2793e-01 . . +X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs FILTER_Mutect2 FILTER_Freebayes FILTER_Vardict FILTER_Varscan m2_MQ m2_MQRankSum m2_TLOD m2_NLOD f_MQM f_MQMR vs_SSC vs_SPV vd_SSF +1 1 100006410 100006410 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.65 9.890 . . . . . +2 1 100060264 100060264 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.67 17.760 . . . . . +3 1 100080141 100080141 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 14.73 13.500 . . . . . +4 1 100092090 100092090 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.21 9.190 . . . . . +5 1 100134429 100134429 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.71 11.090 . . . . . +6 1 100152081 100152081 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.92 11.440 . . . . . +7 1 100174506 100174506 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.70 7.820 . . . . . +8 1 100209733 100209733 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.94 8.730 . . . . . +9 1 100225346 100225346 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.82 15.510 . . . . . +10 1 10022874 10022874 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.86 -1.922 7.12 20.330 . . . . . +11 1 100250155 100250155 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.83 13.200 . . . . . +12 1 100258580 100258580 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.47 9.240 . . . . . +13 1 100296768 100296768 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.01 13.540 . . . . . +14 1 100297044 100297044 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.31 13.240 . . . . . +15 1 100297045 100297045 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.31 13.240 . . . . . +16 1 10033850 10033850 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.36 0.000 8.16 6.920 . . . . . +17 1 100358950 100358950 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.50 10.090 . . . . . +18 1 100383278 100383278 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.53 9.140 . . . . . +19 1 100418794 100418794 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.96 16.110 . . . . . +20 1 100444255 100444255 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.03 16.150 . . . . . +21 1 100470006 100470006 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.81 15.000 . . . . . +22 1 100473149 100473149 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.99 10.230 . . . . . +23 1 10047524 10047524 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.32 11.440 . . . . . +24 1 100479215 100479215 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.17 13.010 . . . . . +25 1 100494646 100494646 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.37 12.800 . . . . . +26 1 100497166 100497166 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.58 11.690 . . . . . +27 1 10055061 10055061 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.239 10.93 16.720 . . . . . +28 1 100577886 100577886 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.90 13.240 . . . . . +29 1 100578957 100578957 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.16 0.528 7.05 28.520 . . . . . +30 1 10058291 10058291 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.51 10.490 . . . . . +31 1 100655405 100655405 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.45 3.220 . . . . . +32 1 100721127 100721127 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.77 8.380 . . . . . +33 1 100734295 100734295 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.21 23.550 . . . . . +34 1 100808158 100808158 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.95 10.390 . . . . . +35 1 100860521 100860521 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.15 11.850 . . . . . +36 1 100892324 100892324 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.79 11.390 . . . . . +37 1 100899307 100899307 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 10.190 . . . . . +38 1 100900987 100900987 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.25 21.880 . . . . . +39 1 10093338 10093338 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.79 22.340 . . . . . +40 1 100985990 100985990 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.22 10.700 . . . . . +41 1 100997475 100997475 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.01 21.620 . . . . . +42 1 10103045 10103045 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 9 1.1102e-01 . +43 1 101046707 101046707 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.56 7.220 . . . . . +44 1 101077751 101077751 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 7.820 . . . . . +45 1 1011858 1011858 NA/T/T/NA NA/C/C/NA FALSE TRUE FALSE FALSE . . . . 40.0000 0.0000 . . 1.00000 +46 1 101200921 101200921 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.09 8.030 . . . . . +47 1 101286523 101286523 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.96 12.600 . . . . . +48 1 101314659 101314659 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.40 12.550 . . . . . +49 1 101327940 101327940 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.66 6.920 . . . . . +50 1 101341644 101341644 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.10 15.300 . . . . . +51 1 1013597 1013597 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 4 3.6774e-01 . +52 1 101386497 101386497 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.06 12.340 . . . . . +53 1 101388692 101388692 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 45.19 -1.821 6.92 9.280 . . . . . +54 1 101447189 101447189 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.54 12.040 . . . . . +55 1 1014491 1014491 NA/NA/NA/A NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 10 9.0194e-02 . +56 1 10145409 10145409 G/NA/G/NA T/NA/T/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.50 13.840 . . . . 0.07507 +57 1 101474973 101474973 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.41 10.180 . . . . . +58 1 101478368 101478368 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.20 14.400 . . . . . +59 1 10148579 10148579 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.60 0.000 8.05 11.500 . . . . . +60 1 10151604 10151604 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.86 9.930 . . . . . +61 1 101521146 101521146 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.37 11.390 . . . . . +62 1 101577254 101577254 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.27 11.740 . . . . . +63 1 101594262 101594262 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.41 10.530 . . . . . +64 1 101614905 101614905 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.65 8.130 . . . . . +65 1 101648707 101648707 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.31 3.870 . . . . . +66 1 101660179 101660179 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.29 14.310 . . . . . +67 1 101686 101686 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 10 8.1600e-02 . +68 1 101737832 101737832 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 54.66 0.869 6.40 4.210 . . . . . +69 1 101792161 101792161 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.91 0.000 8.07 19.520 . . . . . +70 1 101839305 101839305 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.54 11.850 . . . . . +71 1 1018394 1018394 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 4 3.4188e-01 . +72 1 101935915 101935915 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.05 27.410 . . . . . +73 1 101979853 101979853 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.83 8.540 . . . . . +74 1 101988892 101988892 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.83 0.000 7.13 16.240 . . . . . +75 1 102014809 102014809 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 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FALSE FALSE TRUE . . . . . . 9 1.1095e-01 . +760 1 12842353 12842353 T/NA/T/T A/NA/A/A TRUE FALSE FALSE TRUE 53.04 -1.932 7.54 5.010 . . 17 1.7294e-02 0.31360 +761 1 12849501 12849501 C/C/NA/NA T/T/NA/NA FALSE TRUE FALSE FALSE 51.47 -2.237 13.06 7.800 40.8571 46.2703 . . . +762 1 12849604 12849604 NA/NA/G/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00011 +763 1 12849608 12849608 NA/NA/G/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00006 +764 1 12853378 12853378 T/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 55.12 -3.803 10.62 12.610 . . . . . +765 1 12861884 12861884 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 6 2.5088e-01 . +766 1 12885546 12885546 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 7 1.6156e-01 . +767 1 12885551 12885551 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 12 5.8163e-02 . +768 1 12885552 12885552 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 11 6.9683e-02 . +769 1 12888289 12888289 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 44.35 0.039 15.24 6.530 . . . . . +770 1 12890598 12890598 NA/C/C/C NA/T/T/T FALSE FALSE FALSE TRUE . . . . . . 16 2.3525e-02 0.57405 +771 1 12890598 12890598 NA/C/C/C NA/G/T/T FALSE FALSE FALSE TRUE . . . . . . 16 2.3525e-02 0.57405 +772 1 12891787 12891787 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 52.60 -2.799 8.71 23.680 . . . . . +773 1 12892106 12892106 T/NA/T/NA C/NA/C/NA TRUE FALSE FALSE FALSE 57.23 -5.903 8.84 9.920 . . . . 0.24006 +774 1 12894604 12894604 G/NA/G/NA A/NA/A/NA TRUE FALSE TRUE FALSE 54.23 -2.715 6.36 14.090 . . . . 0.02247 +775 1 12894742 12894742 C/C/C/C T/T/T/T TRUE TRUE TRUE TRUE 56.00 -3.440 10.85 10.470 25.3750 48.2941 18 1.4580e-02 0.00538 +776 1 12905405 12905405 C/NA/C/C T/NA/T/T FALSE FALSE FALSE TRUE 47.99 -2.456 4.13 3.260 . . 11 7.7327e-02 0.50202 +777 1 12910888 12910888 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.66 11.990 . . . . . +778 1 12914150 12914150 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.42 0.354 6.85 35.330 . . . . . +779 1 12923959 12923959 NA/NA/C/C NA/NA/G/G FALSE FALSE FALSE TRUE . . . . . . 13 4.3317e-02 0.09875 +780 1 12925279 12925279 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 56.21 -2.180 8.56 8.640 . . . . . +781 1 12925670 12925670 C/NA/C/NA T/NA/T/NA TRUE FALSE FALSE FALSE 52.64 -3.577 7.57 12.640 . . . . 0.31218 +782 1 12938465 12938465 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 13 4.2507e-02 . +783 1 12938473 12938473 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 14 3.3654e-02 . +784 1 12939159 12939159 NA/NA/C/C NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 18 1.3211e-02 0.16172 +785 1 12939904 12939904 A/NA/A/A C/NA/C/C TRUE FALSE FALSE TRUE 50.92 -2.410 10.03 8.370 . . 14 3.4482e-02 0.16373 +786 1 12942710 12942710 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 19 1.1768e-02 . +787 1 12942713 12942713 NA/NA/C/C NA/NA/G/G FALSE FALSE FALSE TRUE . . . . . . 22 5.6867e-03 1.00000 +788 1 12944366 12944366 A/NA/NA/A C/NA/NA/C FALSE FALSE FALSE TRUE 48.23 -1.864 5.22 6.370 . . 16 2.0704e-02 . +789 1 12944377 12944377 NA/NA/A/A NA/NA/C/C FALSE FALSE FALSE TRUE . . . . . . 13 4.7928e-02 0.64308 +790 1 12944833 12944833 NA/NA/C/C NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 23 4.2673e-03 0.08628 +791 1 12944892 12944892 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 55.24 -2.353 10.86 4.310 . . . . . +792 1 12947004 12947004 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.25 -1.590 7.94 3.580 . . . . . +793 1 12949999 12949999 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 51.84 -2.939 7.56 24.840 . . . . . +794 1 1296335 1296335 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.05 -0.080 6.67 33.480 . . . . . +795 1 12967367 12967367 A/A/A/A C/C/C/C FALSE TRUE TRUE TRUE 49.14 -3.679 14.99 4.470 27.5000 41.4783 17 1.6908e-02 0.05250 +796 1 12975323 12975323 NA/NA/T/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.21429 +797 1 12985594 12985594 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.29 0.051 6.91 5.370 . . . . . +798 1 12988822 12988822 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 14 3.1941e-02 . +799 1 12990082 12990082 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 57.46 0.646 8.88 49.430 . . . . . +800 1 13002709 13002709 NA/NA/NA/T NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.9235e-02 . +801 1 13009281 13009281 NA/NA/C/C NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 11 6.9683e-02 0.22581 +802 1 13047590 13047590 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 48.94 -1.301 6.46 6.480 . . . . . +803 1 13051081 13051081 NA/NA/G/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.08767 +804 1 13116267 13116267 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 13 4.0912e-02 . +805 1 13116270 13116270 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 13 4.9909e-02 . +806 1 13116288 13116288 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 12 5.7918e-02 . +807 1 13118773 13118773 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . 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C/NA/NA/C G/NA/NA/G FALSE FALSE FALSE TRUE 58.48 -6.243 5.98 8.410 . . 15 2.8054e-02 . +818 1 13184687 13184687 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 10 9.7959e-02 . +819 1 13189827 13189827 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.154 7.12 27.940 . . . . . +820 1 13205908 13205908 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 6 2.1764e-01 . +821 1 13217549 13217549 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 11 7.3950e-02 . +822 1 1324951 1324951 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.63 21.620 . . . . . +823 1 1336081 1336081 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.10 -0.142 6.89 30.900 . . . . . +824 1 13377172 13377172 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 7 1.9580e-01 . +825 1 13378480 13378480 NA/T/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . . . . . . +826 1 13378481 13378481 NA/T/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . . . . . . +827 1 134496 134496 NA/NA/NA/C 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60.00 0.000 6.68 5.370 . . . . . +1897 1 16831510 16831510 NA/A/A/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 37.3636 58.4103 . . 0.01186 +1898 1 16831572 16831572 NA/C/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . . . . . . +1899 1 16831573 16831573 NA/T/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . . . . . . +1900 1 16831583 16831583 NA/G/G/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 29.8462 59.5077 . . 0.05234 +1901 1 168317293 168317293 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 0.239 6.61 12.500 . . . . . +1902 1 168337681 168337681 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 9.490 . . . . . +1903 1 16834012 16834012 NA/NA/A/A NA/NA/T/T FALSE FALSE TRUE TRUE . . . . . . 23 4.6169e-03 0.01680 +1904 1 16835584 16835584 A/A/NA/NA G/G/NA/NA TRUE FALSE FALSE FALSE 56.86 -5.497 10.55 8.060 . . . . . +1905 1 16836026 16836026 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 52.92 -1.020 9.45 9.050 . . . . . +1906 1 16837823 16837823 NA/G/G/G NA/A/A/A FALSE FALSE FALSE TRUE . . . . 29.6875 31.2302 14 3.5817e-02 0.04186 +1907 1 16838071 16838071 C/NA/C/NA T/NA/T/NA TRUE FALSE FALSE FALSE 55.51 -0.443 41.58 26.530 . . . . 0.16951 +1908 1 16839489 16839489 A/NA/A/NA G/NA/G/NA TRUE FALSE FALSE FALSE 51.73 -1.855 6.39 14.410 . . . . 0.56896 +1909 1 16840226 16840226 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 52.12 -5.254 22.28 12.180 . . . . . +1910 1 168407223 168407223 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.78 0.000 8.13 23.540 . . . . . +1911 1 16841381 16841381 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 51.98 0.980 7.28 30.560 . . . . . +1912 1 16841952 16841952 NA/G/G/G NA/A/A/A FALSE TRUE FALSE TRUE . . . . 33.6364 26.5233 14 3.7240e-02 0.10805 +1913 1 168422263 168422263 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.57 9.280 . . . . . +1914 1 168422408 168422408 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.94 6.830 . . . . . +1915 1 16842968 16842968 NA/NA/C/C NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 16 2.0327e-02 0.06641 +1916 1 168509047 168509047 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.08 12.250 . . . . . +1917 1 168531443 168531443 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 22.39 10.490 . . . . . +1918 1 16855554 16855554 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 8 1.4084e-01 . +1919 1 16856712 16856712 NA/C/C/C NA/T/A/A FALSE FALSE FALSE TRUE . . . . . . 21 6.8339e-03 0.00390 +1920 1 16858329 16858329 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 13 4.4944e-02 . +1921 1 168613652 168613652 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.65 10.790 . . . . . +1922 1 16861614 16861614 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 48.12 -2.468 10.87 11.660 . . . . . +1923 1 16862261 16862261 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 53.00 -3.176 15.15 10.790 . . . . . +1924 1 168624937 168624937 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.18 11.390 . . . . . +1925 1 16863201 16863201 C/NA/NA/C T/NA/NA/T FALSE FALSE FALSE TRUE 46.99 -4.235 5.84 6.920 . . 26 2.1013e-03 . +1926 1 168635009 168635009 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.59 6.020 . . . . . +1927 1 168637825 168637825 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.49 10.440 . . . . . +1928 1 168648467 168648467 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 57.89 0.856 8.80 10.490 . . . . . +1929 1 168650656 168650656 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.54 10.830 . . . . . +1930 1 168698460 168698460 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 10.860 . . . . . +1931 1 168702579 168702579 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.65 15.350 . . . . . +1932 1 16870422 16870422 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 51.84 -1.053 6.71 11.830 . . . . . +1933 1 16870947 16870947 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 50.54 -2.393 13.55 22.390 . . . . . +1934 1 168713570 168713570 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.34 29.860 . . . . . +1935 1 168716055 168716055 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 52.88 1.485 12.47 9.190 . . . . . +1936 1 168726766 168726766 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.18 13.710 . . . . . +1937 1 16874041 16874041 NA/C/C/NA NA/G/G/NA FALSE TRUE FALSE FALSE . . . . 36.0909 36.7222 . . 0.01245 +1938 1 16876705 16876705 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.58 0.571 11.91 20.790 . . . . . +1939 1 16877844 16877844 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 15 3.1241e-02 . +1940 1 16885297 16885297 NA/C/C/C NA/A/A/A FALSE FALSE FALSE TRUE . . . . 49.1923 52.0895 13 4.1865e-02 0.20034 +1941 1 16887040 16887040 NA/A/A/A NA/G/G/G FALSE TRUE FALSE TRUE . . . . 59.6897 58.2463 22 5.5592e-03 0.00947 +1942 1 168871799 168871799 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.69 21.340 . . . . . +1943 1 16890681 16890681 C/NA/C/NA G/NA/G/NA TRUE FALSE FALSE FALSE 54.50 -2.632 21.29 17.480 . . . . 0.29443 +1944 1 168908031 168908031 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.60 31.630 . . . . . +1945 1 16891870 16891870 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.69 -1.920 7.07 88.440 . . . . . +1946 1 168931014 168931014 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.34 16.280 . . . . . +1947 1 16894763 16894763 G/NA/NA/G A/NA/NA/A FALSE FALSE FALSE TRUE 56.66 -4.938 21.61 24.820 . . 14 3.5690e-02 . +1948 1 16897721 16897721 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 50.08 -0.419 7.29 4.790 . . . . . +1949 1 16900847 16900847 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 51.77 -2.081 6.85 30.870 . . . . . +1950 1 16901303 16901303 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 51.63 -2.631 6.83 11.830 . . . . . +1951 1 169029402 169029402 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.83 13.250 . . . . . +1952 1 169034384 169034384 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.15 6.020 . . . . . +1953 1 169036458 169036458 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.34 9.930 . . . . . +1954 1 16903798 16903798 T/NA/NA/T C/NA/NA/C FALSE FALSE FALSE TRUE 51.19 -4.074 27.10 20.760 . . 15 2.5155e-02 . +1955 1 16903803 16903803 T/NA/NA/T C/NA/NA/C FALSE FALSE FALSE TRUE 50.70 -3.780 26.90 20.590 . . 13 4.2013e-02 . +1956 1 16905492 16905492 T/NA/T/NA C/NA/C/NA TRUE FALSE FALSE FALSE 52.84 -2.169 13.09 3.180 . . . . 0.41052 +1957 1 16905788 16905788 A/NA/NA/A G/NA/NA/G FALSE FALSE FALSE TRUE 48.96 -2.716 15.23 15.870 . . 13 4.2483e-02 . +1958 1 16905789 16905789 T/NA/NA/T C/NA/NA/C FALSE FALSE FALSE TRUE 49.14 -2.733 15.23 15.870 . . 14 3.5945e-02 . +1959 1 16905800 16905800 G/NA/NA/G A/NA/NA/A FALSE FALSE FALSE TRUE 49.19 -2.320 13.09 12.700 . . 14 3.4880e-02 . +1960 1 16907164 16907164 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 56.66 0.594 19.23 9.910 . . . . . +1961 1 16907970 16907970 C/NA/NA/C A/NA/NA/A FALSE FALSE FALSE TRUE 53.80 0.329 22.11 15.540 . . 21 7.3898e-03 . +1962 1 16908793 16908793 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 48.60 -1.219 9.08 5.190 . . . . . +1963 1 16909600 16909600 NA/A/A/A NA/C/C/C FALSE FALSE FALSE TRUE . . . . 32.1481 51.6129 13 4.9190e-02 0.21840 +1964 1 16911937 16911937 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 48.68 -0.856 9.05 7.040 . . . . . +1965 1 169121682 169121682 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 11.390 . . . . . +1966 1 169123087 169123087 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.11 5.590 . . . . . +1967 1 16915243 16915243 NA/NA/A/A NA/NA/G/G FALSE FALSE FALSE TRUE . . . . . . 18 1.5580e-02 0.19910 +1968 1 169168864 169168864 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.35 6.650 . . . . . +1969 1 169175169 169175169 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.30 11.440 . . . . . +1970 1 16918895 16918895 NA/C/C/C NA/T/T/T FALSE FALSE FALSE TRUE . . . . 39.7143 41.0062 25 2.7198e-03 0.01140 +1971 1 16919665 16919665 NA/T/T/T NA/C/C/C FALSE FALSE FALSE TRUE . . . . 58.5111 58.2184 13 4.5978e-02 0.10075 +1972 1 169209502 169209502 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.57 8.730 . . . . . +1973 1 169215195 169215195 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 11.090 . . . . . +1974 1 16921601 16921601 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 54.98 1.028 7.39 27.160 . . . . . +1975 1 16922230 16922230 NA/G/G/G NA/C/C/C FALSE FALSE FALSE TRUE . . . . . . 14 3.1661e-02 0.69088 +1976 1 169226138 169226138 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.80 -5.124 11.18 14.740 . . . . . +1977 1 169226327 169226327 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 51.35 -2.842 7.46 10.650 . . . . . +1978 1 16923291 16923291 A/A/A/A G/G/G/G FALSE FALSE FALSE TRUE 52.27 -2.945 79.39 2.100 39.5952 44.1358 21 6.3558e-03 0.00601 +1979 1 16923517 16923517 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 55.62 -2.651 18.90 11.250 . . . . . +1980 1 169248290 169248290 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.207 7.44 27.150 . . . . . +1981 1 169260225 169260225 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.255 7.78 12.290 . . . . . +1982 1 169274196 169274196 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 12.340 . . . . . +1983 1 16928862 16928862 NA/T/T/T NA/C/C/C FALSE FALSE FALSE TRUE . . . . 58.9459 59.2951 20 9.2028e-03 0.01133 +1984 1 16931453 16931453 NA/T/T/T NA/C/C/C FALSE FALSE FALSE TRUE . . . . 60.0000 58.5485 15 3.0773e-02 0.03502 +1985 1 16932859 16932859 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 57.83 -1.258 27.45 3.520 . . . . . +1986 1 16935677 16935677 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.85 41.480 . . . . . +1987 1 16936759 16936759 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.53 55.060 . . . . . +1988 1 169372065 169372065 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 57.19 1.008 11.38 9.280 . . . . . +1989 1 169374673 169374673 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.01 14.450 . . . . . +1990 1 16938426 16938426 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.000 9.01 70.750 . . . . . +1991 1 169412406 169412406 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.97 9.890 . . . . . +1992 1 16942588 16942588 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.03 18.330 . . . . . +1993 1 16945570 16945570 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 49.02 1.078 39.50 10.500 . . . . . +1994 1 169464427 169464427 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.09 20.670 . . . . . +1995 1 169485819 169485819 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.92 12.250 . . . . . +1996 1 16952764 16952764 A/NA/A/NA C/NA/C/NA TRUE FALSE FALSE FALSE 60.00 0.000 24.51 5.610 . . . . 0.75631 +1997 1 169553094 169553094 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.19 12.200 . . . . . +1998 1 169566207 169566207 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.35 10.530 . . . . . +1999 1 16957963 16957963 G/G/G/G A/A/A/A TRUE FALSE FALSE FALSE 59.95 -1.821 24.43 2.590 59.9722 59.8366 3 4.6977e-01 1.00000 +2000 1 16958063 16958063 C/C/NA/NA T/T/NA/NA TRUE FALSE FALSE FALSE 58.78 1.058 34.07 6.180 . . . . . +2001 1 169630082 169630082 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.66 0.397 7.51 21.730 . . . . . +2002 1 16970822 16970822 C/C/C/C A/A/A/A FALSE FALSE FALSE TRUE 59.84 0.924 98.92 6.040 59.1286 59.4047 14 3.9392e-02 0.30341 +2003 1 169730364 169730364 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.13 14.700 . . . . . +2004 1 16974592 16974592 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 7 1.9212e-01 . +2005 1 16975082 16975082 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 46.69 -1.085 14.12 25.530 . . . . . +2006 1 169755504 169755504 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.20 9.630 . . . . . +2007 1 16976436 16976436 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 40.59 -2.164 10.46 16.740 . . . . . +2008 1 169765647 169765647 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 6.920 . . . . . +2009 1 169766146 169766146 T/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.12 11.740 . . . . . +2010 1 16977426 16977426 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 54.68 -1.749 6.40 12.990 . . . . . +2011 1 16979538 16979538 A/NA/NA/A T/NA/NA/T FALSE FALSE FALSE TRUE 45.01 -1.793 5.31 9.540 . . 15 2.7607e-02 . +2012 1 16980198 16980198 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 50.89 0.730 8.08 25.820 . . . . . +2013 1 16982110 16982110 NA/G/G/G NA/A/A/A FALSE TRUE FALSE FALSE . . . . 27.0000 0.0000 0 8.4732e-01 1.00000 +2014 1 169833926 169833926 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.62 0.000 6.87 32.780 . . . . . +2015 1 16983551 16983551 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 5 2.7143e-01 . +2016 1 169854004 169854004 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 10.490 . . . . . +2017 1 16988492 16988492 NA/NA/G/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.23077 +2018 1 16988627 16988627 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 15 3.0672e-02 . +2019 1 169920180 169920180 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.14 6.020 . . . . . +2020 1 169920181 169920181 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.14 6.020 . . . . . +2021 1 169938635 169938635 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.27 17.760 . . . . . +2022 1 169942068 169942068 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.04 6.270 . . . . . +2023 1 169977319 169977319 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.84 13.200 . . . . . +2024 1 169999107 169999107 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.29 11.390 . . . . . +2025 1 17000346 17000346 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 13 4.1253e-02 . +2026 1 170010186 170010186 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.41 0.000 6.88 12.840 . . . . . +2027 1 17001480 17001480 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 55.53 -0.515 7.51 11.940 . . . . . +2028 1 17002002 17002002 NA/NA/C/C NA/NA/G/G FALSE FALSE TRUE FALSE . . . . . . 7 1.9293e-01 0.12488 +2029 1 17004698 17004698 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.99 10.140 . . . . . +2030 1 170081076 170081076 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 57.32 -4.544 8.76 13.750 . . . . . +2031 1 170196665 170196665 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.65 11.560 . . . . . +2032 1 170232986 170232986 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 8.080 . . . . . +2033 1 170248931 170248931 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.248 7.67 14.700 . . . . . +2034 1 170252983 170252983 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.01 11.990 . . . . . +2035 1 170264489 170264489 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.35 11.740 . . . . . +2036 1 170273074 170273074 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.51 9.890 . . . . . +2037 1 170304390 170304390 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.26 -0.230 9.00 15.950 . . . . . +2038 1 170356197 170356197 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.16 0.000 9.01 12.040 . . . . . +2039 1 170441369 170441369 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.41 13.150 . . . . . +2040 1 170447268 170447268 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.64 12.640 . . . . . +2041 1 17053946 17053946 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.92 42.040 . . . . . +2042 1 17055494 17055494 NA/NA/G/G NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 13 4.8606e-02 0.04180 +2043 1 17055499 17055499 NA/NA/G/G NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 14 3.8164e-02 0.07575 +2044 1 17058674 17058674 G/NA/G/G A/NA/A/A TRUE FALSE FALSE TRUE 46.60 -3.507 13.01 10.380 . . 14 3.2040e-02 0.10581 +2045 1 17059929 17059929 C/C/C/C T/T/T/T FALSE FALSE FALSE TRUE 56.63 -2.866 38.51 28.290 52.8022 55.5746 16 2.2097e-02 0.21148 +2046 1 17059970 17059970 G/G/G/G A/A/A/A FALSE FALSE FALSE TRUE 57.65 -6.127 33.36 70.310 55.8690 54.7539 25 2.6711e-03 0.00710 +2047 1 17060050 17060050 G/NA/G/G A/NA/A/A FALSE FALSE FALSE TRUE 43.44 -1.570 69.03 19.130 . . 17 1.9474e-02 0.00312 +2048 1 17061928 17061928 C/NA/NA/C T/NA/NA/T FALSE FALSE FALSE TRUE 46.17 -1.105 20.49 13.020 . . 14 3.5778e-02 . +2049 1 170639044 170639044 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.46 20.160 . . . . . +2050 1 170640745 170640745 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.13 33.780 . . . . . +2051 1 170687597 170687597 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.09 10.230 . . . . . +2052 1 17070222 17070222 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 15 3.0249e-02 . +2053 1 170729300 170729300 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.63 -6.035 7.32 14.400 . . . . . +2054 1 170739387 170739387 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.56 8.730 . . . . . +2055 1 17074777 17074777 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 19 1.0350e-02 . +2056 1 17074789 17074789 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 21 6.7512e-03 . +2057 1 17075448 17075448 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 7 1.6585e-01 . +2058 1 17076425 17076425 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 41.21 0.633 10.07 6.490 . . . . . +2059 1 17077171 17077171 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 41.03 -1.148 26.66 3.900 . . . . . +2060 1 17077221 17077221 NA/NA/G/G NA/NA/A/A FALSE FALSE FALSE TRUE . . . . . . 16 2.3253e-02 0.06347 +2061 1 170783164 170783164 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.86 0.270 7.77 10.830 . . . . . +2062 1 17079458 17079458 C/C/C/NA T/T/T/NA FALSE TRUE FALSE FALSE 48.67 -2.580 23.47 3.660 29.6000 28.9041 . . 0.00804 +2063 1 17079986 17079986 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 45.70 0.663 11.36 10.840 . . . . . +2064 1 17081535 17081535 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. +2672 1 22617536 22617536 T/T/T/NA C/C/C/NA FALSE FALSE TRUE FALSE 60.00 0.000 18.89 1.200 60.0000 60.0000 . . 0.09341 +2673 1 22637265 22637265 T/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.90 12.710 . . . . . +2674 1 22641342 22641342 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.63 23.640 . . . . . +2675 1 22644262 22644262 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.01 20.070 . . . . . +2676 1 22653004 22653004 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 22.640 . . . . . +2677 1 2273103 2273103 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.203 6.94 14.960 . . . . . +2678 1 22731032 22731032 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.57 8.430 . . . . . +2679 1 22736623 22736623 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.97 31.110 . . . . . +2680 1 22747221 22747221 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.50 28.480 . . . . . +2681 1 22785852 22785852 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.67 12.340 . . . . . +2682 1 22800726 22800726 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.89 9.280 . . . . . +2683 1 2286481 2286481 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.34 3.870 . . . . . +2684 1 22873764 22873764 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.14 13.800 . . . . . +2685 1 22881319 22881319 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.77 15.600 . . . . . +2686 1 22900447 22900447 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.72 28.960 . . . . . +2687 1 22904426 22904426 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.71 0.000 8.43 11.550 . . . . . +2688 1 22908994 22908994 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.11 22.690 . . . . . +2689 1 22929585 22929585 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.08 5.420 . . . . . +2690 1 22935005 22935005 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.78 8.380 . . . . . +2691 1 22935863 22935863 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.90 17.480 . . . . . +2692 1 22953368 22953368 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.79 17.990 . . . . . +2693 1 22965684 22965684 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.32 15.910 . . . . . +2694 1 22967201 22967201 NA/T/NA/T NA/G/NA/G FALSE FALSE FALSE TRUE . . . . . . 20 9.8053e-03 . +2695 1 2300064 2300064 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.38 19.470 . . . . . +2696 1 23006631 23006631 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.48 13.570 . . . . . +2697 1 2303118 2303118 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.96 30.030 . . . . . +2698 1 23060409 23060409 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.73 16.020 . . . . . +2699 1 23068182 23068182 NA/C/C/NA NA/A/A/NA FALSE FALSE TRUE FALSE . . . . 52.6429 60.0000 . . 0.00000 +2700 1 230942 230942 A/A/A/A G/G/G/G TRUE TRUE FALSE TRUE 46.66 -2.868 9.40 4.100 23.4444 23.7931 34 3.3284e-04 0.05489 +2701 1 23119682 23119682 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.60 35.930 . . . . . +2702 1 2315236 2315236 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 17.620 . . . . . +2703 1 23180727 23180727 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.06 21.990 . . . . . +2704 1 23210313 23210313 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.19 22.890 . . . . . +2705 1 23241388 23241388 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 20.880 . . . . . +2706 1 23243857 23243857 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.25 14.190 . . . . . +2707 1 23268210 23268210 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 7 1.8347e-01 . +2708 1 23284854 23284854 NA/NA/A/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00771 +2709 1 2328563 2328563 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.50 12.150 . . . . . +2710 1 23404373 23404373 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.61 12.900 . . . . . +2711 1 23415975 23415975 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.26 21.280 . . . . . +2712 1 23423273 23423273 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.63 16.460 . . . . . +2713 1 23437373 23437373 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 8 1.3277e-01 . +2714 1 23447544 23447544 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.63 8.980 . . . . . +2715 1 234575 234575 NA/NA/C/C NA/NA/T/T FALSE FALSE FALSE TRUE . . . . . . 19 1.2094e-02 0.01068 +2716 1 234681 234681 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 49.86 -3.195 6.55 32.880 . . . . . +2717 1 23493288 23493288 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.73 17.020 . . . . . +2718 1 23558044 23558044 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.54 18.520 . . . . . +2719 1 23565128 23565128 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.39 14.520 . . . . . +2720 1 23573794 23573794 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.55 11.950 . . . . . +2721 1 23611725 23611725 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.57 30.170 . . . . . +2722 1 2363638 2363638 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 3 4.3478e-01 . +2723 1 23645254 23645254 C/NA/NA/C A/NA/NA/A TRUE FALSE FALSE TRUE 60.00 0.000 8.65 9.840 . . 7 1.8357e-01 . +2724 1 2367480 2367480 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.39 0.000 7.78 8.430 . . . . . +2725 1 2367794 2367794 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 7 1.8301e-01 . +2726 1 23724814 23724814 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.89 7.940 . . . . . +2727 1 2372495 2372495 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.70 9.240 . . . . . +2728 1 23732540 23732540 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.47 7.080 . . . . . +2729 1 237423 237423 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 17 1.6495e-02 . +2730 1 2374316 2374316 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.66 12.620 . . . . . +2731 1 23755449 23755449 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.77 20.330 . . . . . +2732 1 23801678 23801678 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.56 22.090 . . . . . +2733 1 23809601 23809601 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.62 19.980 . . . . . +2734 1 23830056 23830056 NA/C/NA/C NA/G/NA/G FALSE FALSE FALSE TRUE . . . . 30.3333 40.8182 9 1.1068e-01 . +2735 1 23853127 23853127 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.87 28.060 . . . . . +2736 1 23865612 23865612 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.23 21.830 . . . . . +2737 1 23867232 23867232 NA/T/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 53.6364 57.5600 . . . +2738 1 2390863 2390863 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 5 2.5180e-01 . +2739 1 2390865 2390865 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 6 2.4488e-01 . +2740 1 2390879 2390879 NA/G/G/G NA/C/C/C FALSE TRUE FALSE FALSE . . . . . . 15 2.9503e-02 0.00000 +2741 1 2390881 2390881 NA/C/C/C NA/T/T/T FALSE TRUE FALSE TRUE . . . . . . 21 6.6029e-03 0.00000 +2742 1 2390888 2390888 NA/C/C/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 43.3077 42.3673 . . 0.00000 +2743 1 23908941 23908941 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.75 13.750 . . . . . +2744 1 2390904 2390904 NA/T/NA/T NA/C/NA/C FALSE FALSE FALSE TRUE . . . . 38.7805 45.0375 31 7.8455e-04 . +2745 1 23956916 23956916 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.57 19.030 . . . . . +2746 1 23976578 23976578 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.84 10.490 . . . . . +2747 1 23976936 23976936 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.06 27.990 . . . . . +2748 1 23998317 23998317 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.81 12.500 . . . . . +2749 1 24017332 24017332 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.99 28.550 . . . . . +2750 1 24027511 24027511 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 18.360 . . . . . +2751 1 24028586 24028586 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.55 23.330 . . . . . +2752 1 24030212 24030212 NA/G/G/NA NA/A/A/NA FALSE TRUE FALSE FALSE . . . . 53.2500 0.0000 . . 1.00000 +2753 1 24030233 24030233 NA/C/C/NA NA/T/T/NA FALSE TRUE FALSE FALSE . . . . 51.0000 0.0000 . . 1.00000 +2754 1 24032510 24032510 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.03 -0.301 6.61 17.520 . . . . . +2755 1 24060340 24060340 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.15 10.530 . . . . . +2756 1 2406707 2406707 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.20 9.240 . . . . . +2757 1 24076736 24076736 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.29 0.500 6.39 16.270 . . . . . +2758 1 24084745 24084745 NA/A/A/NA NA/T/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00000 +2759 1 241164 241164 NA/C/C/NA NA/T/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00002 +2760 1 24146073 24146073 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.88 0.257 7.11 19.470 . . . . . +2761 1 24163846 24163846 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 11 6.8747e-02 . +2762 1 24173282 24173282 G/NA/NA/G T/NA/NA/T FALSE FALSE FALSE TRUE 60.00 0.000 5.37 11.600 . . 9 1.0734e-01 . +2763 1 24195349 24195349 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.79 22.530 . . . . . +2764 1 24216775 24216775 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 5 2.5676e-01 . +2765 1 24226389 24226389 NA/NA/G/G NA/NA/A/A FALSE FALSE FALSE TRUE . . . . . . 8 1.2821e-01 0.15172 +2766 1 24234077 24234077 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 9 1.0476e-01 . +2767 1 2423876 2423876 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.22 13.710 . . . . . +2768 1 24239680 24239680 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.14 -0.169 7.65 21.910 . . . . . +2769 1 24249359 24249359 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 8 1.3564e-01 . +2770 1 24282839 24282839 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 41.98 -2.552 12.60 2.710 . . . . . +2771 1 24290061 24290061 NA/G/G/NA NA/C/C/NA FALSE TRUE FALSE FALSE . . . . 35.6667 0.0000 . . 1.00000 +2772 1 24354725 24354725 NA/A/A/A NA/G/G/G FALSE TRUE FALSE FALSE . . . . 27.0000 0.0000 9 1.0868e-01 1.00000 +2773 1 24358372 24358372 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 4 3.1818e-01 . +2774 1 24406387 24406387 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.15 20.240 . . . . . +2775 1 24423561 24423561 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.91 33.270 . . . . . +2776 1 24433197 24433197 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.210 6.95 15.630 . . . . . +2777 1 24494635 24494635 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.43 23.150 . . . . . +2778 1 24537045 24537045 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.81 20.970 . . . . . +2779 1 24545797 24545797 NA/C/NA/C NA/T/NA/T FALSE TRUE FALSE TRUE . . . . 49.6667 62.1538 6 2.4074e-01 . +2780 1 24545807 24545807 NA/T/T/T NA/C/C/C FALSE FALSE TRUE TRUE . . . . . . 6 2.4138e-01 0.00316 +2781 1 24594976 24594976 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.02 14.700 . . . . . +2782 1 24614071 24614071 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.72 6.690 . . . . . +2783 1 24627820 24627820 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.52 19.270 . . . . . +2784 1 24631639 24631639 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.97 8.980 . . . . . +2785 1 24638383 24638383 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.00 20.950 . . . . . +2786 1 24671670 24671670 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 3 4.5333e-01 . +2787 1 24674947 24674947 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.45 31.830 . . . . . +2788 1 24675175 24675175 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.64 26.510 . . . . . +2789 1 24688081 24688081 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.86 7.040 . . . . . +2790 1 24748579 24748579 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.92 33.870 . . . . . +2791 1 24748694 24748694 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.88 26.300 . . . . . +2792 1 24754714 24754714 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 58.48 0.000 6.78 2.710 . . . . . +2793 1 24815445 24815445 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.33 25.150 . . . . . +2794 1 24819748 24819748 C/NA/NA/C A/NA/NA/A TRUE FALSE FALSE TRUE 60.00 0.000 9.03 20.920 . . 13 4.5662e-02 . +2795 1 24837137 24837137 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.92 10.530 . . . . . +2796 1 24839410 24839410 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.71 21.690 . . . . . +2797 1 24859203 24859203 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 57.33 0.000 6.59 4.420 . . . . . +2798 1 24899625 24899625 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.99 18.710 . . . . . +2799 1 24949963 24949963 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.42 13.100 . . . . . +2800 1 24981426 24981426 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 10 9.9351e-02 . +2801 1 25010815 25010815 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.94 0.204 6.44 27.600 . . . . . +2802 1 25021659 25021659 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.96 -5.944 7.82 14.260 . . . . . +2803 1 25029372 25029372 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.35 25.850 . . . . . +2804 1 250301 250301 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 13 4.2576e-02 . +2805 1 25058997 25058997 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.18 21.830 . . . . . +2806 1 25083433 25083433 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.53 10.100 . . . . . +2807 1 25139537 25139537 NA/C/C/NA NA/T/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00000 +2808 1 25144027 25144027 G/NA/NA/G T/NA/NA/T FALSE FALSE FALSE TRUE 60.00 0.000 5.38 11.850 . . 11 6.5278e-02 . +2809 1 251803 251803 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 21 7.5586e-03 . +2810 1 25202507 25202507 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 12 5.0879e-02 . +2811 1 252205 252205 NA/G/G/G NA/A/A/A FALSE TRUE TRUE TRUE . . . . 22.4286 23.2105 19 1.1949e-02 0.00739 +2812 1 25222763 25222763 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.41 25.130 . . . . . +2813 1 25229309 25229309 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.37 4.930 . . . . . +2814 1 25282478 25282478 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.45 26.300 . . . . . +2815 1 25322776 25322776 C/C/NA/C T/T/NA/T TRUE FALSE FALSE TRUE 60.00 0.000 178.96 23.850 . . 139 1.0804e-14 . +2816 1 2533531 2533531 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.50 32.530 . . . . . +2817 1 25340636 25340636 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.76 20.480 . . . . . +2818 1 25341492 25341492 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.49 20.230 . . . . . +2819 1 25345392 25345392 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.97 37.080 . . . . . +2820 1 25348769 25348769 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 3 4.5833e-01 . +2821 1 25353235 25353235 NA/T/T/T NA/A/A/A FALSE FALSE TRUE FALSE . . . . 60.0000 60.0000 0 1.0000e+00 0.00000 +2822 1 25380177 25380177 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.45 15.860 . . . . . +2823 1 25393944 25393944 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.28 25.770 . . . . . +2824 1 25405764 25405764 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.51 7.780 . . . . . +2825 1 25406224 25406224 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.79 0.270 8.89 13.660 . . . . . +2826 1 25426358 25426358 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.27 9.650 . . . . . +2827 1 25428507 25428507 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.60 12.850 . . . . . +2828 1 25441835 25441835 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.34 6.180 . . . . . +2829 1 25449498 25449498 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.09 11.550 . . . . . +2830 1 254728 254728 NA/NA/T/T NA/NA/G/G FALSE FALSE TRUE FALSE . . . . . . 8 1.3823e-01 0.02232 +2831 1 25475191 25475191 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.62 11.800 . . . . . +2832 1 25482689 25482689 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.93 16.510 . . . . . +2833 1 25511225 25511225 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.140 6.69 31.970 . . . . . +2834 1 255185 255185 G/NA/G/G A/NA/A/A FALSE FALSE FALSE TRUE 46.70 -1.464 5.92 10.410 . . 14 3.6232e-02 0.18600 +2835 1 25542041 25542041 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.38 8.330 . . . . . +2836 1 25543390 25543390 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.00 18.610 . . . . . +2837 1 255593 255593 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 21 7.5805e-03 . +2838 1 25573061 25573061 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 13.660 . . . . . +2839 1 255897 255897 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 11 7.6276e-02 . +2840 1 25638219 25638219 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 49.14 -1.915 6.93 11.690 . . . . . +2841 1 25648090 25648090 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.90 3.570 . . . . . +2842 1 2569600 2569600 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.55 9.280 . . . . . +2843 1 25696816 25696816 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 53.00 -2.356 7.42 14.740 . . . . . +2844 1 25725136 25725136 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 37.67 -2.183 6.32 10.490 . . . . . +2845 1 25741764 25741764 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 52.92 1.632 6.85 20.620 . . . . . +2846 1 25837445 25837445 NA/NA/A/NA NA/NA/G/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.06591 +2847 1 25837785 25837785 NA/NA/A/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.23404 +2848 1 25837821 25837821 NA/NA/C/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.10694 +2849 1 2583802 2583802 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 48 1.2738e-05 . +2850 1 2583829 2583829 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 82 5.8125e-09 . +2851 1 2585364 2585364 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 13 4.1068e-02 . +2852 1 25855031 25855031 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 14.440 . . . . . +2853 1 2585751 2585751 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 14 3.4903e-02 . +2854 1 2585991 2585991 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 35 2.9900e-04 . +2855 1 25860532 25860532 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.68 21.880 . . . . . +2856 1 2586067 2586067 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 33 4.1375e-04 . +2857 1 25863189 25863189 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.02 14.450 . . . . . +2858 1 2586374 2586374 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 23.11 2.767 9.19 30.810 . . . . . +2859 1 2586414 2586414 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 71 6.4674e-08 . +2860 1 25866594 25866594 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.29 14.050 . . . . . +2861 1 2586860 2586860 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 37 1.8622e-04 . +2862 1 2586913 2586913 T/NA/NA/T G/NA/NA/G TRUE FALSE FALSE FALSE 23.24 -0.473 15.00 53.910 . . 1 7.9206e-01 . +2863 1 2586947 2586947 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 22.49 1.299 8.79 22.590 . . . . . +2864 1 2587086 2587086 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 32 5.9203e-04 . +2865 1 2587371 2587371 C/NA/NA/C T/NA/NA/T FALSE FALSE FALSE TRUE 33.15 -7.151 36.06 27.200 . . 61 7.1461e-07 . +2866 1 2587407 2587407 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 42 5.6934e-05 . +2867 1 2587408 2587408 C/NA/NA/C T/NA/NA/A FALSE FALSE FALSE TRUE 31.19 -1.287 4.84 14.410 . . 34 3.8986e-04 . +2868 1 2587996 2587996 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 7 1.5909e-01 . +2869 1 2588607 2588607 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.7232e-02 . +2870 1 25888735 25888735 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.36 17.710 . . . . . +2871 1 2589814 2589814 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 13 4.8627e-02 . +2872 1 2589830 2589830 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 15 3.1275e-02 . +2873 1 25904275 25904275 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.64 17.390 . . . . . +2874 1 2590948 2590948 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 15 2.5857e-02 . +2875 1 2590988 2590988 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 19 1.1974e-02 . +2876 1 2591273 2591273 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 15 2.7431e-02 . +2877 1 2591363 2591363 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 14 3.9135e-02 . +2878 1 2591422 2591422 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 25 2.8419e-03 . +2879 1 2591603 2591603 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 5 2.7027e-01 . +2880 1 2591606 2591606 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 8 1.3514e-01 . +2881 1 2591607 2591607 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 5 2.8529e-01 . +2882 1 2591739 2591739 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 26 2.4809e-03 . +2883 1 25919113 25919113 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.94 0.248 7.13 18.510 . . . . . +2884 1 2592314 2592314 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 15 3.0535e-02 . +2885 1 2592394 2592394 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 13 4.4736e-02 . +2886 1 25927191 25927191 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.30 7.180 . . . . . +2887 1 2593541 2593541 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 15 3.0813e-02 . +2888 1 2594234 2594234 NA/NA/NA/A NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 20 9.5297e-03 . +2889 1 25952357 25952357 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.95 11.950 . . . . . +2890 1 25957178 25957178 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.00 11.090 . . . . . +2891 1 25981440 25981440 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.85 0.214 11.42 27.970 . . . . . +2892 1 2600562 2600562 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 24 3.3747e-03 . +2893 1 26031728 26031728 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 14.700 . . . . . +2894 1 2603318 2603318 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 27.97 -6.089 44.55 57.720 . . . . . +2895 1 26043096 26043096 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.41 12.290 . . . . . +2896 1 2606567 2606567 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 26 2.3961e-03 . +2897 1 26066386 26066386 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.50 31.090 . . . . . +2898 1 2606687 2606687 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 17 1.8155e-02 . +2899 1 26067946 26067946 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.83 18.130 . . . . . +2900 1 2606946 2606946 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 26 2.0706e-03 . +2901 1 2606994 2606994 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 18.75 -3.995 7.31 6.440 . . . . . +2902 1 2607101 2607101 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 19 1.0217e-02 . +2903 1 2607399 2607399 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 18 1.5482e-02 . +2904 1 2607404 2607404 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.4181e-02 . +2905 1 2607406 2607406 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 24 3.8020e-03 . +2906 1 2607415 2607415 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 15 3.1381e-02 . +2907 1 2609077 2609077 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 21 7.9373e-03 . +2908 1 2609185 2609185 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 13 4.1666e-02 . +2909 1 2609405 2609405 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 15 3.0097e-02 . +2910 1 26096281 26096281 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.40 6.830 . . . . . +2911 1 26112928 26112928 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.81 24.010 . . . . . +2912 1 2611617 2611617 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 18 1.3135e-02 . +2913 1 2611620 2611620 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.3706e-02 . +2914 1 2611640 2611640 NA/NA/NA/T NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 22 5.5874e-03 . +2915 1 26116680 26116680 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.49 24.500 . . . . . +2916 1 2611808 2611808 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 13 4.7029e-02 . +2917 1 2614235 2614235 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 14 3.8932e-02 . +2918 1 2614428 2614428 NA/NA/NA/A NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 14 3.7440e-02 . +2919 1 2615474 2615474 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 14 3.4217e-02 . +2920 1 2615635 2615635 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 13 4.6403e-02 . +2921 1 2615995 2615995 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 44.73 -3.820 6.78 11.400 . . . . . +2922 1 26164548 26164548 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.189 7.09 15.190 . . . . . +2923 1 2616707 2616707 G/NA/NA/G A/NA/NA/A TRUE FALSE FALSE FALSE 28.95 -0.060 11.37 12.970 . . 4 3.3972e-01 . +2924 1 26168907 26168907 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.72 9.330 . . . . . +2925 1 2617274 2617274 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.5469e-02 . +2926 1 2617353 2617353 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 13 4.5382e-02 . +2927 1 2617373 2617373 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 17 1.8894e-02 . +2928 1 2617382 2617382 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 38 1.3651e-04 . +2929 1 2617436 2617436 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 24.29 -0.713 32.74 6.260 . . . . . +2930 1 2617672 2617672 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 13 4.7108e-02 . +2931 1 2618229 2618229 NA/NA/NA/T NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 15 2.5747e-02 . +2932 1 2618269 2618269 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 21 7.0034e-03 . +2933 1 2618438 2618438 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 18 1.3950e-02 . +2934 1 2618492 2618492 T/NA/NA/T A/NA/NA/A TRUE FALSE FALSE FALSE 30.43 -2.247 37.77 6.060 . . 40 9.7074e-05 . +2935 1 26186009 26186009 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.03 2.710 . . . . . +2936 1 2618834 2618834 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 28 1.2874e-03 . +2937 1 26189429 26189429 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.69 26.900 . . . . . +2938 1 2619596 2619596 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 20 9.6328e-03 . +2939 1 2619614 2619614 C/NA/NA/C T/NA/NA/T FALSE FALSE FALSE TRUE 27.99 -2.760 22.22 17.610 . . 28 1.4849e-03 . +2940 1 2619622 2619622 G/NA/NA/G T/NA/NA/T FALSE FALSE FALSE TRUE 26.82 -3.060 18.40 27.770 . . 18 1.3000e-02 . +2941 1 26198633 26198633 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.38 28.200 . . . . . +2942 1 2620447 2620447 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 13 4.7337e-02 . +2943 1 26209387 26209387 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 12 5.8140e-02 . +2944 1 2621498 2621498 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 39 1.1363e-04 . +2945 1 2621688 2621688 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 25 2.6908e-03 . +2946 1 2622110 2622110 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 14 3.6165e-02 . +2947 1 2622170 2622170 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 31 7.3970e-04 . +2948 1 2622177 2622177 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 33 4.6814e-04 . +2949 1 2622179 2622179 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 26 2.1809e-03 . +2950 1 26221876 26221876 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.51 26.620 . . . . . +2951 1 2622211 2622211 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 23 4.2612e-03 . +2952 1 2622398 2622398 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 24.05 -0.404 10.90 14.170 . . . . . +2953 1 2622836 2622836 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 24 3.7411e-03 . +2954 1 26228559 26228559 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.64 15.050 . . . . . +2955 1 2622877 2622877 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 17 1.6866e-02 . +2956 1 2622907 2622907 T/NA/NA/T G/NA/NA/G TRUE FALSE FALSE TRUE 45.89 -10.119 25.20 5.320 . . 20 8.9132e-03 . +2957 1 2622939 2622939 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 14 3.8508e-02 . +2958 1 2623503 2623503 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 24.74 -3.003 30.36 63.880 . . . . . +2959 1 2623545 2623545 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 18 1.5151e-02 . +2960 1 2624174 2624174 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 15 2.6762e-02 . +2961 1 2624696 2624696 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 22 5.9460e-03 . +2962 1 2624975 2624975 G/NA/NA/G A/NA/NA/A TRUE FALSE FALSE FALSE 15.62 -0.568 9.73 8.810 . . 16 2.3090e-02 . +2963 1 2625036 2625036 NA/NA/NA/A NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 15 2.8618e-02 . +2964 1 2625267 2625267 C/NA/NA/C G/NA/NA/A TRUE FALSE FALSE FALSE 21.16 -1.908 20.06 10.530 . . 11 6.7283e-02 . +2965 1 2625719 2625719 NA/NA/NA/G NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 23 4.4154e-03 . +2966 1 2625729 2625729 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 30 8.3435e-04 . +2967 1 26261899 26261899 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.02 7.130 . . . . . +2968 1 2626292 2626292 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 40.93 -3.018 8.99 5.960 . . . . . +2969 1 2626535 2626535 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 18 1.4486e-02 . +2970 1 2626684 2626684 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 20 8.7926e-03 . +2971 1 2627358 2627358 NA/NA/NA/C NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 15 2.6815e-02 . +2972 1 2627368 2627368 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 18.45 -2.280 13.63 11.760 . . . . . +2973 1 2627894 2627894 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 14 3.8579e-02 . +2974 1 2628253 2628253 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 44.89 -0.018 10.42 97.870 . . . . . +2975 1 2628558 2628558 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 24.60 -2.316 26.21 45.530 . . . . . +2976 1 2628602 2628602 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 27.86 -2.187 25.88 43.650 . . . . . +2977 1 2628703 2628703 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 18 1.5313e-02 . +2978 1 2628781 2628781 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 23 4.9136e-03 . +2979 1 2628785 2628785 NA/NA/NA/C NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 37 1.9576e-04 . +2980 1 2629540 2629540 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 25 2.5834e-03 . +2981 1 26365692 26365692 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.88 22.760 . . . . . +2982 1 26379647 26379647 NA/NA/C/NA NA/NA/A/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.01069 +2983 1 26427394 26427394 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 11 7.5188e-02 . +2984 1 26497159 26497159 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7.51 17.020 . . . . . +4519 1 663755 663755 NA/NA/NA/G NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 10 9.7778e-02 . +4520 1 66445070 66445070 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 8.590 . . . . . +4521 1 66456606 66456606 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.58 11.690 . . . . . +4522 1 66457500 66457500 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.72 19.120 . . . . . +4523 1 6651517 6651517 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.93 18.150 . . . . . +4524 1 66541377 66541377 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.53 9.450 . . . . . +4525 1 66542775 66542775 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.61 12.590 . . . . . +4526 1 66627167 66627167 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.51 13.410 . . . . . +4527 1 66630493 66630493 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.38 0.538 11.64 8.070 . . . . . +4528 1 666848 666848 NA/G/G/G NA/C/C/C FALSE TRUE FALSE FALSE . . . . 20.3077 27.6000 22 5.2174e-03 0.08301 +4529 1 6675653 6675653 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 16 2.2876e-02 . +4530 1 66836833 66836833 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.78 5.070 . . . . . +4531 1 66853627 66853627 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.94 9.330 . . . . . +4532 1 6687999 6687999 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.98 15.540 . . . . . +4533 1 66881145 66881145 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.65 13.500 . . . . . +4534 1 66952927 66952927 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.09 9.630 . . . . . +4535 1 66967965 66967965 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.21 13.150 . . . . . +4536 1 6701464 6701464 NA/T/T/NA NA/C/C/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00799 +4537 1 6701466 6701466 NA/NA/T/NA NA/NA/C/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00024 +4538 1 670571 670571 NA/NA/NA/C NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 14 3.5326e-02 . +4539 1 67089428 67089428 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 44.09 16.720 . . . . . +4540 1 67127021 67127021 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.40 7.470 . . . . . +4541 1 67136153 67136153 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 11.690 . . . . . +4542 1 67162141 67162141 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.30 12.550 . . . . . +4543 1 67163154 67163154 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.09 9.630 . . . . . +4544 1 67168256 67168256 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.47 11.990 . . . . . +4545 1 67238601 67238601 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.81 13.310 . . . . . +4546 1 67251853 67251853 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 49.92 0.521 6.70 7.110 . . . . . +4547 1 67341820 67341820 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.11 5.670 . . . . . +4548 1 67371744 67371744 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.95 0.208 6.38 24.700 . . . . . +4549 1 6737235 6737235 NA/C/C/NA NA/A/A/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00158 +4550 1 67382863 67382863 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.95 11.740 . . . . . +4551 1 67402262 67402262 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.41 21.280 . . . . . +4552 1 67481302 67481302 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.48 0.000 8.66 10.740 . . . . . +4553 1 67577401 67577401 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.61 7.830 . . . . . +4554 1 67578030 67578030 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.27 14.010 . . . . . +4555 1 67596895 67596895 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.86 15.510 . . . . . +4556 1 67624615 67624615 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 51.95 0.907 7.06 19.090 . . . . . +4557 1 67671644 67671644 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.58 0.343 7.22 25.180 . . . . . +4558 1 67696692 67696692 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 9.930 . . . . . +4559 1 67771013 67771013 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 15.030 . . . . . +4560 1 6777617 6777617 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.46 12.940 . . . . . +4561 1 67797998 67797998 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.16 4.655 8.92 13.270 . . . . . +4562 1 67807813 67807813 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.21 7.730 . . . . . +4563 1 6781144 6781144 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.06 19.330 . . . . . +4564 1 67827520 67827520 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 29.560 . . . . . +4565 1 67901795 67901795 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.82 -5.523 6.32 25.760 . . . . . +4566 1 67916411 67916411 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.13 8.630 . . . . . +4567 1 67924797 67924797 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.26 15.960 . . . . . +4568 1 68005203 68005203 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.42 27.940 . . . . . +4569 1 68024830 68024830 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.25 -0.224 8.75 13.270 . . . . . +4570 1 68030170 68030170 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.91 15.250 . . . . . +4571 1 68054063 68054063 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.67 10.390 . . . . . +4572 1 68066379 68066379 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.173 7.33 24.960 . . . . . +4573 1 68088369 68088369 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.88 8.590 . . . . . +4574 1 68102558 68102558 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 14.100 . . . . . +4575 1 68118805 68118805 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.03 9.840 . . . . . +4576 1 68174701 68174701 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.24 20.230 . . . . . +4577 1 68183768 68183768 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.61 0.000 8.70 12.040 . . . . . +4578 1 68212753 68212753 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.78 9.040 . . . . . +4579 1 68227444 68227444 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 15.42 14.350 . . . . . +4580 1 6826109 6826109 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.15 9.450 . . . . . +4581 1 68275970 68275970 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.12 10.400 . . . . . +4582 1 68288240 68288240 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.16 12.640 . . . . . +4583 1 6828944 6828944 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.07 -0.119 6.69 32.640 . . . . . +4584 1 68390630 68390630 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.64 11.990 . . . . . +4585 1 68436222 68436222 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.77 15.300 . . . . . +4586 1 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9.580 . . . . . +5438 1 924281 924281 NA/T/T/T NA/G/G/G FALSE FALSE FALSE TRUE . . . . 58.9333 59.5932 13 4.2868e-02 0.70647 +5439 1 92459681 92459681 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.82 11.390 . . . . . +5440 1 92497539 92497539 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.93 14.010 . . . . . +5441 1 92547468 92547468 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.97 0.154 7.24 29.560 . . . . . +5442 1 92584457 92584457 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.87 -0.275 9.02 10.440 . . . . . +5443 1 92596327 92596327 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.84 0.291 8.57 12.800 . . . . . +5444 1 92629987 92629987 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.00 15.210 . . . . . +5445 1 92683327 92683327 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.59 11.900 . . . . . +5446 1 92687677 92687677 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.68 23.750 . . . . . +5447 1 92729973 92729973 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.45 21.140 . . . . . +5448 1 92730444 92730444 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.89 0.249 6.63 27.320 . . . . . +5449 1 92741181 92741181 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.58 9.890 . . . . . +5450 1 92781177 92781177 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.08 12.290 . . . . . +5451 1 9283868 9283868 NA/NA/C/NA NA/NA/T/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00019 +5452 1 92891012 92891012 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.38 13.200 . . . . . +5453 1 92902557 92902557 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.70 12.300 . . . . . +5454 1 92947423 92947423 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.97 19.260 . . . . . +5455 1 92981844 92981844 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.91 7.850 . . . . . +5456 1 92985425 92985425 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.46 9.280 . . . . . +5457 1 93002676 93002676 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.02 7.830 . . . . . +5458 1 9302846 9302846 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.60 14.660 . . . . . +5459 1 93035144 93035144 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.85 0.136 6.99 39.700 . . . . . +5460 1 93055124 93055124 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.58 0.401 8.29 8.730 . . . . . +5461 1 93092806 93092806 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.05 0.504 8.47 9.930 . . . . . +5462 1 93158250 93158250 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 10.190 . . . . . +5463 1 93181721 93181721 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.90 -9.128 6.79 20.540 . . . . . +5464 1 93183779 93183779 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 58.83 0.677 7.36 8.380 . . . . . +5465 1 93214552 93214552 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.38 0.471 8.02 10.090 . . . . . +5466 1 93223308 93223308 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 13.65 10.840 . . . . . +5467 1 93400221 93400221 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.52 15.000 . . . . . +5468 1 9341005 9341005 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.20 26.860 . . . . . +5469 1 93451051 93451051 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.05 22.940 . . . . . +5470 1 9345728 9345728 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.67 14.350 . . . . . +5471 1 93463208 93463208 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.16 11.390 . . . . . +5472 1 9351284 9351284 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 59.42 0.000 10.25 3.730 . . . . . +5473 1 93559306 93559306 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.30 7.680 . . . . . +5474 1 93560788 93560788 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 17.360 . . . . . +5475 1 9357648 9357648 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.12 10.530 . . . . . 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FALSE FALSE 60.00 0.000 6.54 22.730 . . . . . +5486 1 9380981 9380981 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 7 1.6368e-01 . +5487 1 93841649 93841649 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.14 29.100 . . . . . +5488 1 9386676 9386676 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.68 26.080 . . . . . +5489 1 93880753 93880753 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.70 12.940 . . . . . +5490 1 93952097 93952097 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.29 17.060 . . . . . +5491 1 93964452 93964452 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 9.490 . . . . . +5492 1 94000972 94000972 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.38 12.900 . . . . . +5493 1 94079456 94079456 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.89 20.530 . . . . . +5494 1 94080498 94080498 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.46 12.290 . . . . . +5495 1 94146330 94146330 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.48 21.990 . . . . . +5496 1 9416705 9416705 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.61 16.970 . . . . . +5497 1 9416954 9416954 NA/G/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . . . . . . +5498 1 94198653 94198653 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.66 11.040 . . . . . +5499 1 94347076 94347076 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.44 11.090 . . . . . +5500 1 94347252 94347252 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.07 11.340 . . . . . +5501 1 94369513 94369513 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.85 9.190 . . . . . +5502 1 94391096 94391096 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.54 10.400 . . . . . +5503 1 9440261 9440261 NA/C/C/C NA/G/G/G FALSE FALSE FALSE TRUE . . . . 46.6923 57.1000 15 2.6696e-02 0.03569 +5504 1 9440263 9440263 NA/A/NA/NA NA/G/NA/NA FALSE TRUE FALSE FALSE . . . . 35.0000 54.6957 . . . +5505 1 9440332 9440332 NA/G/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 57.1429 47.8333 . . . +5506 1 9440338 9440338 NA/G/NA/NA NA/A/NA/NA FALSE TRUE FALSE FALSE . . . . 57.7778 47.7656 . . . +5507 1 94434577 94434577 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.13 12.800 . . . . . +5508 1 94450709 94450709 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.33 17.360 . . . . . +5509 1 94451116 94451116 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.74 -5.066 6.89 24.490 . . . . . +5510 1 94461769 94461769 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.53 28.550 . . . . . +5511 1 94502668 94502668 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.17 7.690 . . . . . +5512 1 94502931 94502931 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.36 17.270 . . . . . +5513 1 94546557 94546557 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.69 0.195 6.83 25.650 . . . . . +5514 1 94547686 94547686 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.58 12.040 . . . . . +5515 1 94552179 94552179 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.70 12.760 . . . . . +5516 1 94564649 94564649 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.28 21.950 . . . . . +5517 1 9457410 9457410 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.80 0.211 7.26 20.630 . . . . . +5518 1 9464402 9464402 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.40 25.140 . . . . . +5519 1 9465205 9465205 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.62 28.450 . . . . . +5520 1 94700775 94700775 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.36 12.500 . . . . . +5521 1 94715138 94715138 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.91 -11.660 7.43 24.280 . . . . . +5522 1 9478609 9478609 A/A/A/A G/G/G/G TRUE TRUE TRUE TRUE 59.04 0.000 40.12 6.620 56.6842 59.1714 57 1.6063e-06 0.00000 +5523 1 94844907 94844907 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.47 16.510 . . . . . +5524 1 94887850 94887850 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.71 19.820 . . . . . +5525 1 94941475 94941475 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.47 7.520 . . . . . +5526 1 94998215 94998215 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.06 23.940 . . . . . +5527 1 95005698 95005698 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.63 13.960 . . . . . +5528 1 95019120 95019120 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.71 34.080 . . . . . +5529 1 95021000 95021000 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.53 11.990 . . . . . +5530 1 9505959 9505959 NA/C/NA/NA NA/T/NA/NA FALSE TRUE FALSE FALSE . . . . 47.0625 57.3953 . . . +5531 1 95072928 95072928 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.40 8.940 . . . . . +5532 1 95087159 95087159 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.67 24.130 . . . . . +5533 1 95093083 95093083 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.64 12.200 . . . . . +5534 1 95168051 95168051 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.38 18.430 . . . . . +5535 1 95185134 95185134 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 6.830 . . . . . +5536 1 95232032 95232032 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.90 12.850 . . . . . +5537 1 95274996 95274996 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.97 9.490 . . . . . +5538 1 95275734 95275734 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.50 6.780 . . . . . +5539 1 95308504 95308504 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.07 42.900 . . . . . +5540 1 9534933 9534933 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.80 21.690 . . . . . +5541 1 95360291 95360291 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 35.53 9.150 . . . . . +5542 1 9541005 9541005 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.43 20.470 . . . . . +5543 1 9543518 9543518 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.11 20.330 . . . . . +5544 1 95484018 95484018 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.18 11.650 . . . . . +5545 1 95487473 95487473 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.56 11.340 . . . . . +5546 1 95532400 95532400 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.44 6.320 . . . . . +5547 1 95578483 95578483 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.98 0.157 6.41 28.710 . . . . . +5548 1 95593804 95593804 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.20 9.330 . . . . . +5549 1 9562429 9562429 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.32 16.510 . . . . . +5550 1 95650707 95650707 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.20 12.500 . . . . . +5551 1 95659992 95659992 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.14 -0.135 8.67 12.760 . . . . . +5552 1 95675096 95675096 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.85 10.530 . . . . . +5553 1 95701009 95701009 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 57.98 0.534 9.50 11.730 . . . . . +5554 1 95875801 95875801 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.83 41.350 . . . . . +5555 1 95914537 95914537 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.73 19.420 . . . . . +5556 1 9596773 9596773 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.74 18.060 . . . . . +5557 1 96058611 96058611 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.09 6.690 . . . . . +5558 1 96098671 96098671 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.50 0.000 8.59 6.620 . . . . . +5559 1 96102496 96102496 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.53 7.520 . . . . . +5560 1 96184411 96184411 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.85 11.000 . . . . . +5561 1 961953 961953 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 5 2.7143e-01 . +5562 1 96221394 96221394 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.59 12.550 . . . . . +5563 1 96289393 96289393 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.65 11.140 . . . . . +5564 1 96289394 96289394 A/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.65 11.140 . . . . . +5565 1 96372619 96372619 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.93 10.840 . . . . . +5566 1 9637837 9637837 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.34 23.590 . . . . . +5567 1 96404226 96404226 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.84 15.600 . . . . . +5568 1 96449240 96449240 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.75 10.790 . . . . . +5569 1 9645077 9645077 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.71 13.200 . . . . . +5570 1 96474292 96474292 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.49 5.920 . . . . . +5571 1 96474503 96474503 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.99 11.950 . . . . . +5572 1 965417 965417 NA/NA/NA/T NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 13 4.5086e-02 . +5573 1 96563186 96563186 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.00 8.680 . . . . . +5574 1 96598811 96598811 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.99 9.630 . . . . . +5575 1 96620232 96620232 C/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 7.220 . . . . . +5576 1 96626974 96626974 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.45 8.730 . . . . . +5577 1 966307 966307 NA/G/G/G NA/A/A/A FALSE FALSE FALSE TRUE . . . . 37.7391 40.8393 14 3.7138e-02 0.39023 +5578 1 96654390 96654390 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.00 12.340 . . . . . +5579 1 96722379 96722379 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.25 10.700 . . . . . +5580 1 96766147 96766147 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.55 17.620 . . . . . +5581 1 96817440 96817440 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.36 8.340 . . . . . +5582 1 96836579 96836579 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.000 6.55 19.730 . . . . . +5583 1 96839638 96839638 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.57 14.860 . . . . . +5584 1 96898926 96898926 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.70 7.680 . . . . . +5585 1 96924254 96924254 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.77 11.140 . . . . . +5586 1 96934826 96934826 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 58.21 0.726 9.48 5.630 . . . . . +5587 1 96954406 96954406 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.31 15.260 . . . . . +5588 1 96981061 96981061 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.60 20.670 . . . . . +5589 1 96981155 96981155 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.50 16.370 . . . . . +5590 1 97013059 97013059 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 15.650 . . . . . +5591 1 97013294 97013294 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.02 7.480 . . . . . +5592 1 97015725 97015725 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.91 12.900 . . . . . +5593 1 97064036 97064036 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.70 7.180 . . . . . +5594 1 9706973 9706973 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 11 7.9426e-02 . +5595 1 97092553 97092553 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.05 10.530 . . . . . +5596 1 9711356 9711356 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.39 16.810 . . . . . +5597 1 97126506 97126506 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 60.45 8.120 . . . . . +5598 1 97149410 97149410 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.74 14.610 . . . . . +5599 1 97227512 97227512 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 47.45 -2.725 8.23 7.180 . . . . . +5600 1 97237777 97237777 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.47 9.280 . . . . . +5601 1 97253482 97253482 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.10 9.890 . . . . . +5602 1 97305793 97305793 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.73 12.850 . . . . . +5603 1 97314437 97314437 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.57 29.660 . . . . . +5604 1 97316712 97316712 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.50 10.790 . . . . . +5605 1 9733474 9733474 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.01 22.570 . . . . . +5606 1 97341078 97341078 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.44 10.490 . . . . . +5607 1 97342756 97342756 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.83 7.780 . . . . . +5608 1 97347 97347 NA/NA/NA/T NA/NA/NA/A FALSE FALSE FALSE TRUE . . . . . . 21 7.0229e-03 . +5609 1 97377558 97377558 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.57 11.430 . . . . . +5610 1 97415456 97415456 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.33 9.790 . . . . . +5611 1 97424328 97424328 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.43 9.630 . . . . . +5612 1 97443832 97443832 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.86 10.400 . . . . . +5613 1 97480755 97480755 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.93 15.610 . . . . . +5614 1 9755554 9755554 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.28 27.600 . . . . . +5615 1 97617846 97617846 C/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 16.85 7.470 . . . . . +5616 1 97637720 97637720 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.65 10.340 . . . . . +5617 1 9770714 9770714 NA/C/C/NA NA/G/G/NA FALSE FALSE TRUE FALSE . . . . . . . . 0.00314 +5618 1 97745321 97745321 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.34 25.350 . . . . . +5619 1 97776335 97776335 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.78 10.230 . . . . . +5620 1 97879547 97879547 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.67 8.940 . . . . . +5621 1 97950799 97950799 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.76 21.550 . . . . . +5622 1 97980323 97980323 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.35 11.340 . . . . . +5623 1 97995921 97995921 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.34 -3.234 6.48 27.970 . . . . . +5624 1 98006863 98006863 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.74 11.040 . . . . . +5625 1 98035836 98035836 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.67 12.940 . . . . . +5626 1 9809793 9809793 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.31 20.970 . . . . . +5627 1 98123031 98123031 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.69 12.850 . . . . . +5628 1 9814508 9814508 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 12 5.9322e-02 . +5629 1 9817122 9817122 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.213 7.09 33.870 . . . . . +5630 1 98177332 98177332 A/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 11.740 . . . . . +5631 1 98177333 98177333 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.94 11.740 . . . . . +5632 1 98191239 98191239 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.77 0.000 7.24 19.520 . . . . . +5633 1 98224311 98224311 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.82 10.090 . . . . . +5634 1 98241684 98241684 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.82 11.990 . . . . . +5635 1 98256537 98256537 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 10.07 12.850 . . . . . +5636 1 98260367 98260367 T/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.82 11.990 . . . . . +5637 1 98263533 98263533 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.83 6.620 . . . . . +5638 1 98277488 98277488 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 10.530 . . . . . +5639 1 98305795 98305795 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.31 9.030 . . . . . +5640 1 9836280 9836280 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.36 0.473 6.62 19.090 . . . . . +5641 1 98413446 98413446 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.82 7.480 . . . . . +5642 1 98420721 98420721 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.24 8.430 . . . . . +5643 1 98423769 98423769 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 11.62 9.030 . . . . . +5644 1 98456116 98456116 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.80 10.390 . . . . . +5645 1 98467343 98467343 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.09 12.340 . . . . . +5646 1 98498629 98498629 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.25 10.830 . . . . . +5647 1 98512918 98512918 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.95 8.120 . . . . . +5648 1 98537802 98537802 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.27 8.330 . . . . . +5649 1 9855804 9855804 NA/NA/NA/G NA/NA/NA/T FALSE FALSE FALSE TRUE . . . . . . 11 7.5188e-02 . +5650 1 98598355 98598355 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 13.850 . . . . . +5651 1 98599804 98599804 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.05 13.200 . . . . . +5652 1 98618373 98618373 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.93 11.140 . . . . . +5653 1 98619399 98619399 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 52.85 -2.047 7.36 10.830 . . . . . +5654 1 98620378 98620378 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.45 10.230 . . . . . +5655 1 98632380 98632380 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 54.66 -2.611 9.14 3.170 . . . . . +5656 1 98660550 98660550 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.46 12.650 . . . . . +5657 1 9879741 9879741 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.07 12.340 . . . . . +5658 1 98833555 98833555 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.37 18.120 . . . . . +5659 1 98839389 98839389 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.76 16.710 . . . . . +5660 1 988589 988589 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.43 29.720 . . . . . +5661 1 98887732 98887732 T/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.38 12.910 . . . . . +5662 1 98901222 98901222 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.79 10.190 . . . . . +5663 1 98922909 98922909 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.02 12.040 . . . . . +5664 1 9892447 9892447 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.84 0.293 7.67 22.640 . . . . . +5665 1 98955927 98955927 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 10.140 . . . . . +5666 1 9901778 9901778 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.62 34.610 . . . . . +5667 1 99078743 99078743 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.23 -6.625 8.60 12.340 . . . . . +5668 1 99110323 99110323 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.39 12.500 . . . . . +5669 1 99122432 99122432 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 59.92 0.248 7.03 19.220 . . . . . +5670 1 9915195 9915195 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.44 10.470 . . . . . +5671 1 991740 991740 NA/NA/NA/T NA/NA/NA/G FALSE FALSE FALSE TRUE . . . . . . 3 4.8718e-01 . +5672 1 9919213 9919213 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.82 21.390 . . . . . +5673 1 99197309 99197309 A/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.24 17.970 . . . . . +5674 1 99200411 99200411 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.17 11.040 . . . . . +5675 1 99211202 99211202 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.51 13.360 . . . . . +5676 1 9923608 9923608 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.25 13.450 . . . . . +5677 1 99243125 99243125 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.24 11.000 . . . . . +5678 1 99248349 99248349 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.36 10.840 . . . . . +5679 1 9926261 9926261 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.31 17.570 . . . . . +5680 1 99283498 99283498 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.50 41.410 . . . . . +5681 1 9930056 9930056 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.47 22.690 . . . . . +5682 1 99346747 99346747 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 59.93 0.282 8.28 19.540 . . . . . +5683 1 9935359 9935359 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.65 13.570 . . . . . +5684 1 99366649 99366649 G/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.21 10.740 . . . . . +5685 1 9944161 9944161 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.53 9.790 . . . . . +5686 1 9945523 9945523 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 9.96 25.490 . . . . . +5687 1 99466079 99466079 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 7.43 5.320 . . . . . +5688 1 99645342 99645342 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.68 10.790 . . . . . +5689 1 99699311 99699311 T/NA/NA/NA G/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.56 5.250 . . . . . +5690 1 9971265 9971265 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.40 21.930 . . . . . +5691 1 99715853 99715853 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.51 8.640 . . . . . +5692 1 99759054 99759054 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.16 9.330 . . . . . +5693 1 99773620 99773620 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.42 9.280 . . . . . +5694 1 99844197 99844197 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 6.62 35.720 . . . . . +5695 1 99864301 99864301 C/NA/NA/NA A/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.14 15.860 . . . . . +5696 1 9987947 9987947 G/G/G/G C/C/C/C TRUE TRUE TRUE TRUE 60.00 0.000 10.36 3.770 60.0000 58.8140 24 3.6125e-03 0.00401 +5697 1 99880333 99880333 G/NA/NA/NA C/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 12.03 10.490 . . . . . +5698 1 99924239 99924239 G/NA/NA/NA T/NA/NA/NA TRUE FALSE FALSE FALSE 60.00 0.000 8.85 15.210 . . . . . +5699 1 9993308 9993308 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 4 3.4476e-01 . +5700 1 9993311 9993311 NA/NA/NA/A NA/NA/NA/C FALSE FALSE FALSE TRUE . . . . . . 6 2.2793e-01 . diff --git a/test/results/snv-predicted.txt b/test/results/snv-predicted.txt index 4529410..255eb09 100644 --- a/test/results/snv-predicted.txt +++ b/test/results/snv-predicted.txt @@ -1,13 +1,400 @@ -X.CHROM START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs TRUTH_confidence -1 1 12207135 12207135 G/G/G/G A/A/A/A 0.9941938 -2 1 14955425 14955425 C/C/C/C A/A/A/A 0.9025974 -3 1 18525077 18525077 G/G/G/G A/A/A/A 0.9972492 -4 1 21459584 21459584 T/T/T/T A/A/A/A 0.9919866 -5 1 2180985 2180985 A/A/A/A G/G/G/G 0.9992510 -6 1 22385823 22385823 A/A/A/A G/G/G/G 0.6207352 -7 1 25322776 25322776 C/C/NA/C T/T/NA/T 0.8995001 -8 1 28317030 28317030 G/NA/G/G T/NA/T/T 0.8962453 -9 1 5035185 5035185 C/C/C/C T/T/T/T 0.9321060 -10 1 8881322 8881322 G/G/G/G A/A/A/A 0.9116895 -11 1 8929624 8929624 A/A/A/A G/G/G/G 0.8765643 -12 1 9478609 9478609 A/A/A/A G/G/G/G 0.5984848 +Chr START_POS_REF END_POS_REF REF_MFVdVs ALT_MFVdVs SMuRF_score +1 1 100080141 100080141 T/NA/NA/NA A/NA/NA/NA 0.5449806 +2 1 100418794 100418794 G/NA/NA/NA T/NA/NA/NA 0.4698960 +3 1 100444255 100444255 A/NA/NA/NA T/NA/NA/NA 0.4725965 +4 1 100470006 100470006 C/NA/NA/NA A/NA/NA/NA 0.4074448 +5 1 100494646 100494646 G/NA/NA/NA T/NA/NA/NA 0.3901333 +6 1 100997475 100997475 C/NA/NA/NA A/NA/NA/NA 0.4804897 +7 1 101341644 101341644 C/NA/NA/NA A/NA/NA/NA 0.4275855 +8 1 10145409 10145409 G/NA/G/NA T/NA/T/NA 0.3965020 +9 1 10207357 10207357 C/NA/NA/NA A/NA/NA/NA 0.4614254 +10 1 102105563 102105563 G/NA/NA/NA A/NA/NA/NA 0.4074448 +11 1 102126778 102126778 T/NA/NA/NA 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G/NA/NA/NA A/NA/NA/NA 0.5838542 +256 1 4873590 4873590 C/NA/NA/NA A/NA/NA/NA 0.3917556 +257 1 5035185 5035185 C/C/C/C T/T/T/T 0.9942729 +258 1 51328036 51328036 A/NA/NA/NA T/NA/NA/NA 0.4725965 +259 1 51406053 51406053 C/NA/NA/NA A/NA/NA/NA 0.4314701 +260 1 51493180 51493180 C/NA/NA/NA T/NA/NA/NA 0.4074448 +261 1 51687593 51687593 C/NA/NA/NA T/NA/NA/NA 0.4546415 +262 1 51770010 51770010 C/NA/NA/NA A/NA/NA/NA 0.4004201 +263 1 52379899 52379899 G/NA/NA/NA T/NA/NA/NA 0.4725965 +264 1 52526401 52526401 G/NA/NA/NA T/NA/NA/NA 0.4237504 +265 1 52782336 52782336 G/NA/NA/NA T/NA/NA/NA 0.3939684 +266 1 53373800 53373800 G/NA/NA/NA T/NA/NA/NA 0.4287695 +267 1 5342673 5342673 G/NA/NA/NA T/NA/NA/NA 0.3917556 +268 1 53644152 53644152 G/NA/NA/NA T/NA/NA/NA 0.4926129 +269 1 5458698 5458698 G/NA/NA/NA T/NA/NA/NA 0.4862359 +270 1 54649771 54649771 G/NA/NA/NA T/NA/NA/NA 0.4287695 +271 1 54742455 54742455 C/NA/NA/NA A/NA/NA/NA 0.5220247 +272 1 55161117 55161117 G/NA/NA/NA A/NA/NA/NA 0.4824901 +273 1 55293904 55293904 G/NA/NA/NA C/NA/NA/NA 0.4314701 +274 1 55340888 55340888 C/NA/NA/NA A/NA/NA/NA 0.5220247 +275 1 55347359 55347359 C/NA/NA/NA A/NA/NA/NA 0.4405837 +276 1 55442673 55442673 C/NA/NA/NA A/NA/NA/NA 0.3917556 +277 1 55572220 55572220 C/NA/NA/NA T/NA/NA/NA 0.4239567 +278 1 55812399 55812399 A/NA/NA/NA T/NA/NA/NA 0.4948880 +279 1 55983733 55983733 G/NA/NA/NA T/NA/NA/NA 0.5220247 +280 1 56145665 56145665 G/NA/NA/NA T/NA/NA/NA 0.4074448 +281 1 56463963 56463963 C/NA/NA/NA A/NA/NA/NA 0.4889364 +282 1 56785308 56785308 G/NA/NA/NA A/NA/NA/NA 0.4451554 +283 1 5779742 5779742 G/NA/NA/NA T/NA/NA/NA 0.4138058 +284 1 57945357 57945357 C/NA/NA/NA A/NA/NA/NA 0.4862359 +285 1 58683206 58683206 G/NA/NA/NA T/NA/NA/NA 0.3917556 +286 1 59847424 59847424 T/NA/NA/NA C/NA/NA/NA 0.3939684 +287 1 59942315 59942315 A/NA/NA/NA T/NA/NA/NA 0.3890550 +288 1 6035845 6035845 C/NA/NA/NA A/NA/NA/NA 0.4287695 +289 1 60590090 60590090 G/NA/NA/NA T/NA/NA/NA 0.4889364 +290 1 61281623 61281623 G/NA/NA/NA T/NA/NA/NA 0.4074448 +291 1 61493555 61493555 G/NA/NA/NA T/NA/NA/NA 0.4725965 +292 1 62077480 62077480 G/NA/NA/NA T/NA/NA/NA 0.4074448 +293 1 62120555 62120555 G/NA/NA/NA T/NA/NA/NA 0.4287695 +294 1 62621212 62621212 C/NA/NA/NA A/NA/NA/NA 0.5994790 +295 1 63317897 63317897 G/NA/NA/NA T/NA/NA/NA 0.4275855 +296 1 63477913 63477913 C/NA/NA/NA A/NA/NA/NA 0.4889364 +297 1 63909830 63909830 C/NA/NA/NA A/NA/NA/NA 0.3879205 +298 1 64288164 64288164 A/NA/NA/NA T/NA/NA/NA 0.4275855 +299 1 64572499 64572499 G/NA/NA/NA T/NA/NA/NA 0.3879205 +300 1 64588945 64588945 G/NA/NA/NA T/NA/NA/NA 0.5220247 +301 1 65018792 65018792 C/NA/NA/NA T/NA/NA/NA 0.5416676 +302 1 65057608 65057608 A/NA/NA/NA T/NA/NA/NA 0.3879205 +303 1 65674729 65674729 G/NA/NA/NA T/NA/NA/NA 0.4287695 +304 1 65898551 65898551 C/NA/NA/NA A/NA/NA/NA 0.4900118 +305 1 66060148 66060148 T/NA/NA/NA C/NA/NA/NA 0.5449806 +306 1 6608086 6608086 C/NA/NA/NA A/NA/NA/NA 0.4725965 +307 1 67578030 67578030 G/NA/NA/NA T/NA/NA/NA 0.3917556 +308 1 67596895 67596895 G/NA/NA/NA T/NA/NA/NA 0.4275855 +309 1 6777617 6777617 G/NA/NA/NA T/NA/NA/NA 0.4049978 +310 1 68030170 68030170 G/NA/NA/NA T/NA/NA/NA 0.4275855 +311 1 68227444 68227444 G/NA/NA/NA T/NA/NA/NA 0.6144781 +312 1 68436222 68436222 C/NA/NA/NA A/NA/NA/NA 0.4237504 +313 1 68517759 68517759 G/NA/NA/NA T/NA/NA/NA 0.4022584 +314 1 68704665 68704665 G/NA/NA/NA T/NA/NA/NA 0.4569236 +315 1 68816059 68816059 G/NA/NA/NA T/NA/NA/NA 0.4074448 +316 1 69083465 69083465 C/NA/NA/NA A/NA/NA/NA 0.3917556 +317 1 69816953 69816953 C/NA/NA/NA A/NA/NA/NA 0.4074448 +318 1 70070002 70070002 T/NA/NA/NA A/NA/NA/NA 0.4553071 +319 1 70071723 70071723 C/NA/NA/NA A/NA/NA/NA 0.3917556 +320 1 70708377 70708377 C/NA/NA/NA G/NA/NA/NA 0.4275855 +321 1 71229601 71229601 G/NA/NA/NA T/NA/NA/NA 0.3901333 +322 1 71381177 71381177 T/NA/NA/NA A/NA/NA/NA 0.3917556 +323 1 71381178 71381178 G/NA/NA/NA T/NA/NA/NA 0.3917556 +324 1 7145327 7145327 G/NA/NA/NA T/NA/NA/NA 0.3917556 +325 1 73112675 73112675 C/NA/NA/NA A/NA/NA/NA 0.4725965 +326 1 73190641 73190641 A/NA/NA/NA C/NA/NA/NA 0.4698960 +327 1 73413115 73413115 C/NA/NA/NA A/NA/NA/NA 0.4624666 +328 1 74235713 74235713 G/NA/NA/NA T/NA/NA/NA 0.4846529 +329 1 74928288 74928288 G/NA/NA/NA T/NA/NA/NA 0.3939684 +330 1 75358043 75358043 A/NA/NA/NA T/NA/NA/NA 0.4960945 +331 1 7571655 7571655 C/NA/NA/NA A/NA/NA/NA 0.4237504 +332 1 76363667 76363667 C/NA/NA/NA A/NA/NA/NA 0.4282522 +333 1 76817412 76817412 G/NA/NA/NA T/NA/NA/NA 0.4433849 +334 1 77712621 77712621 G/NA/NA/NA A/NA/NA/NA 0.4387128 +335 1 78007388 78007388 C/NA/NA/NA T/NA/NA/NA 0.4239567 +336 1 78160947 78160947 C/NA/NA/NA G/NA/NA/NA 0.4725965 +337 1 78409357 78409357 C/NA/NA/NA A/NA/NA/NA 0.3939684 +338 1 78721799 78721799 C/NA/NA/NA A/NA/NA/NA 0.3989984 +339 1 7978839 7978839 G/NA/NA/NA T/NA/NA/NA 0.4777891 +340 1 80136620 80136620 A/NA/NA/NA C/NA/NA/NA 0.4486621 +341 1 81074337 81074337 G/NA/NA/NA T/NA/NA/NA 0.4424995 +342 1 81908058 81908058 C/NA/NA/NA A/NA/NA/NA 0.4074448 +343 1 83318093 83318093 C/NA/NA/NA A/NA/NA/NA 0.4074448 +344 1 84037452 84037452 G/NA/NA/NA T/NA/NA/NA 0.3939684 +345 1 84130714 84130714 C/NA/NA/NA A/NA/NA/NA 0.4074448 +346 1 84224682 84224682 A/NA/NA/NA T/NA/NA/NA 0.4074448 +347 1 84277133 84277133 C/NA/NA/NA A/NA/NA/NA 0.4184743 +348 1 84719119 84719119 G/NA/NA/NA T/NA/NA/NA 0.4074448 +349 1 85317660 85317660 G/NA/NA/NA T/NA/NA/NA 0.5156010 +350 1 85414001 85414001 C/NA/NA/NA A/NA/NA/NA 0.4259290 +351 1 85425438 85425438 C/NA/NA/NA A/NA/NA/NA 0.4569236 +352 1 85501786 85501786 C/NA/NA/NA A/NA/NA/NA 0.5018805 +353 1 86089522 86089522 G/NA/NA/NA A/NA/NA/NA 0.3939684 +354 1 8638951 8638951 G/NA/NA/NA T/NA/NA/NA 0.3901333 +355 1 86654794 86654794 G/NA/NA/NA T/NA/NA/NA 0.4275855 +356 1 86754951 86754951 C/NA/NA/NA T/NA/NA/NA 0.4862359 +357 1 86904026 86904026 C/NA/NA/NA A/NA/NA/NA 0.5299815 +358 1 8701077 8701077 C/NA/NA/NA A/NA/NA/NA 0.3917556 +359 1 87421495 87421495 C/NA/NA/NA A/NA/NA/NA 0.5994790 +360 1 88695653 88695653 G/NA/NA/NA T/NA/NA/NA 0.4862359 +361 1 88791506 88791506 C/NA/NA/NA A/NA/NA/NA 0.3939684 +362 1 8881322 8881322 G/G/G/G A/A/A/A 0.9102914 +363 1 88862078 88862078 G/NA/NA/NA A/NA/NA/NA 0.4530783 +364 1 89205444 89205444 G/NA/NA/NA T/NA/NA/NA 0.4725965 +365 1 89254279 89254279 C/NA/NA/NA A/NA/NA/NA 0.4900118 +366 1 89295961 89295961 G/NA/NA/NA T/NA/NA/NA 0.4237504 +367 1 8929624 8929624 A/A/A/A G/G/G/G 0.9240989 +368 1 89390037 89390037 C/NA/NA/NA A/NA/NA/NA 0.5220247 +369 1 90034365 90034365 G/NA/NA/NA T/NA/NA/NA 0.3917556 +370 1 9030469 9030469 G/NA/NA/NA T/NA/NA/NA 0.4926129 +371 1 90344776 90344776 G/NA/NA/NA T/NA/NA/NA 0.4081115 +372 1 90492912 90492912 G/NA/NA/NA T/NA/NA/NA 0.3939684 +373 1 92403269 92403269 T/NA/NA/NA A/NA/NA/NA 0.3912678 +374 1 92497539 92497539 G/NA/NA/NA T/NA/NA/NA 0.3917556 +375 1 92891012 92891012 C/NA/NA/NA T/NA/NA/NA 0.4863308 +376 1 92947423 92947423 G/NA/NA/NA T/NA/NA/NA 0.5193241 +377 1 93451051 93451051 C/NA/NA/NA A/NA/NA/NA 0.4287695 +378 1 93880753 93880753 G/NA/NA/NA T/NA/NA/NA 0.4553071 +379 1 93952097 93952097 G/NA/NA/NA T/NA/NA/NA 0.4889364 +380 1 94146330 94146330 C/NA/NA/NA A/NA/NA/NA 0.4496114 +381 1 9416705 9416705 G/NA/NA/NA T/NA/NA/NA 0.4405837 +382 1 94450709 94450709 T/NA/NA/NA C/NA/NA/NA 0.4569236 +383 1 94502931 94502931 C/NA/NA/NA A/NA/NA/NA 0.4889364 +384 1 9478609 9478609 A/A/A/A G/G/G/G 0.4771242 +385 1 95232032 95232032 C/NA/NA/NA A/NA/NA/NA 0.3939684 +386 1 9534933 9534933 C/NA/NA/NA A/NA/NA/NA 0.5258782 +387 1 9637837 9637837 C/NA/NA/NA A/NA/NA/NA 0.4314701 +388 1 96766147 96766147 C/NA/NA/NA A/NA/NA/NA 0.4494018 +389 1 96981155 96981155 G/NA/NA/NA T/NA/NA/NA 0.4698960 +390 1 97015725 97015725 C/NA/NA/NA A/NA/NA/NA 0.3901333 +391 1 9733474 9733474 C/NA/NA/NA A/NA/NA/NA 0.4314701 +392 1 97480755 97480755 C/NA/NA/NA A/NA/NA/NA 0.4275855 +393 1 97745321 97745321 C/NA/NA/NA A/NA/NA/NA 0.4314701 +394 1 97950799 97950799 G/NA/NA/NA T/NA/NA/NA 0.4926129 +395 1 98256537 98256537 C/NA/NA/NA A/NA/NA/NA 0.3912678 +396 1 98839389 98839389 G/NA/NA/NA T/NA/NA/NA 0.4725965 +397 1 9919213 9919213 C/NA/NA/NA A/NA/NA/NA 0.4899123 +398 1 9945523 9945523 G/NA/NA/NA T/NA/NA/NA 0.4287695 +399 1 99924239 99924239 G/NA/NA/NA T/NA/NA/NA 0.4074448 diff --git a/test/results/snv-stats.txt b/test/results/snv-stats.txt index 5cce2af..f3d9f70 100644 --- a/test/results/snv-stats.txt +++ b/test/results/snv-stats.txt @@ -2,9 +2,9 @@ Passed_Calls Mutect2 5004 FreeBayes 115 VarDict 124 -VarScan 501 -Atleast1 5684 -Atleast2 42 -Atleast3 16 -All4 2 -Model 12 +VarScan 535 +Atleast1 5700 +Atleast2 49 +Atleast3 19 +All4 10 +SMuRF_SNV 399