diff --git a/data/modules/bcftools/issue_1832/bcftools_stats_output.txt b/data/modules/bcftools/issue_1832/bcftools_stats_output.txt new file mode 100644 index 00000000..ee76818f --- /dev/null +++ b/data/modules/bcftools/issue_1832/bcftools_stats_output.txt @@ -0,0 +1,3292 @@ +# This file was produced by bcftools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-vcfstats. +# The command line was: bcftools stats --split-by-ID -s testvcf testvcf.vcf.gz +# +# Definition of sets: +# ID [2]id [3]tab-separated file names +ID 0 testvcf.vcf.gz:known (sites with ID different from ".") +ID 1 testvcf.vcf.gz:novel (sites where ID column is ".") +# SN, Summary numbers: +# SN [2]id [3]key [4]value +SN 0 number of samples: 1 +SN 0 number of records: 4633169 +SN 0 number of no-ALTs: 0 +SN 0 number of SNPs: 3824714 +SN 0 number of MNPs: 0 +SN 0 number of indels: 812623 +SN 0 number of others: 0 +SN 0 number of multiallelic sites: 60701 +SN 0 number of multiallelic SNP sites: 1324 +SN 1 number of records: 228016 +SN 1 number of no-ALTs: 0 +SN 1 number of SNPs: 99291 +SN 1 number of MNPs: 0 +SN 1 number of indels: 129176 +SN 1 number of others: 0 +SN 1 number of multiallelic sites: 13187 +SN 1 number of multiallelic SNP sites: 81 +# TSTV, transitions/transversions: +# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT) +TSTV 0 2564747 1261291 2.03 2563771 1259722 2.04 +TSTV 1 56774 42598 1.33 56573 42377 1.33 +# SiS, Singleton stats: +# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +SiS 0 1 2342505 1571049 771456 562686 0 0 562686 +SiS 1 1 91183 52102 39081 112490 0 0 112490 +# AF, Stats by non-reference allele frequency: +# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +AF 0 0.000000 2342505 1571049 771456 562686 0 0 562686 +AF 0 99.000000 1483533 993698 489835 305146 0 0 305146 +AF 1 0.000000 91183 52102 39081 112490 0 0 112490 +AF 1 99.000000 8189 4672 3517 29341 0 0 29341 +# QUAL, Stats by quality: +# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels +QUAL 0 10 337 193 144 139 +QUAL 0 11 400 239 161 163 +QUAL 0 12 545 334 211 242 +QUAL 0 13 356 215 141 143 +QUAL 0 14 247 141 106 116 +QUAL 0 15 347 217 130 119 +QUAL 0 16 408 247 161 148 +QUAL 0 17 240 143 97 140 +QUAL 0 18 470 288 182 144 +QUAL 0 19 378 228 150 162 +QUAL 0 20 245 153 92 164 +QUAL 0 21 365 228 137 179 +QUAL 0 22 408 266 142 194 +QUAL 0 23 255 154 101 147 +QUAL 0 24 351 210 141 157 +QUAL 0 25 435 261 174 166 +QUAL 0 26 262 161 101 141 +QUAL 0 27 363 223 140 133 +QUAL 0 28 440 282 158 178 +QUAL 0 29 252 156 96 138 +QUAL 0 30 365 221 144 180 +QUAL 0 31 435 265 170 203 +QUAL 0 32 281 178 103 155 +QUAL 0 33 385 240 145 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26 80 +QUAL 1 543 68 42 25 93 +QUAL 1 544 84 51 33 117 +QUAL 1 545 50 31 19 95 +QUAL 1 546 76 47 29 109 +QUAL 1 547 73 38 34 190 +QUAL 1 548 59 32 26 76 +QUAL 1 549 65 42 23 98 +QUAL 1 550 65 46 19 124 +QUAL 1 551 61 40 21 98 +QUAL 1 552 91 61 29 80 +QUAL 1 553 70 39 31 111 +QUAL 1 554 56 33 22 97 +QUAL 1 555 77 50 27 89 +QUAL 1 556 114 62 52 91 +QUAL 1 557 59 38 20 91 +QUAL 1 558 82 50 32 79 +QUAL 1 559 73 44 29 89 +QUAL 1 560 55 31 24 92 +QUAL 1 561 75 51 24 82 +QUAL 1 562 71 45 26 121 +QUAL 1 563 65 45 20 83 +QUAL 1 564 77 50 26 98 +QUAL 1 565 76 48 26 108 +QUAL 1 566 53 31 22 75 +QUAL 1 567 73 48 25 80 +QUAL 1 568 80 52 27 114 +QUAL 1 569 62 38 24 74 +QUAL 1 570 85 49 36 102 +QUAL 1 571 60 30 29 95 +QUAL 1 572 49 30 19 76 +QUAL 1 573 71 40 31 81 +QUAL 1 574 73 48 25 104 +QUAL 1 575 55 36 19 78 +QUAL 1 576 73 49 24 86 +QUAL 1 577 77 55 20 115 +QUAL 1 578 53 33 18 83 +QUAL 1 579 66 47 19 91 +QUAL 1 580 64 45 19 92 +QUAL 1 581 79 49 30 79 +QUAL 1 582 77 48 29 96 +QUAL 1 583 75 43 32 107 +QUAL 1 584 53 35 18 73 +QUAL 1 585 80 46 34 82 +QUAL 1 586 77 46 31 105 +QUAL 1 587 58 45 12 89 +QUAL 1 588 68 44 24 96 +QUAL 1 589 71 45 26 100 +QUAL 1 590 72 36 35 71 +QUAL 1 591 82 55 27 96 +QUAL 1 592 76 48 27 179 +QUAL 1 593 75 51 24 95 +QUAL 1 594 71 42 29 103 +QUAL 1 595 81 54 27 106 +QUAL 1 596 74 49 25 84 +QUAL 1 597 73 43 30 96 +QUAL 1 598 65 44 21 95 +QUAL 1 599 68 42 26 60 +QUAL 1 600 55 37 18 84 +QUAL 1 601 119 62 57 98 +QUAL 1 602 71 46 24 79 +QUAL 1 603 83 57 26 75 +QUAL 1 604 89 55 34 93 +QUAL 1 605 75 53 22 58 +QUAL 1 606 81 52 28 87 +QUAL 1 607 69 41 27 112 +QUAL 1 608 96 63 33 79 +QUAL 1 609 72 47 25 77 +QUAL 1 610 80 51 29 91 +QUAL 1 611 48 28 20 67 +QUAL 1 612 87 56 31 82 +QUAL 1 613 86 48 38 88 +QUAL 1 614 76 43 33 83 +QUAL 1 615 74 42 32 88 +QUAL 1 616 79 47 32 102 +QUAL 1 617 75 39 35 81 +QUAL 1 618 76 48 28 84 +QUAL 1 619 84 52 31 87 +QUAL 1 620 51 32 19 90 +QUAL 1 621 74 48 25 99 +QUAL 1 622 83 49 33 107 +QUAL 1 623 70 42 28 77 +QUAL 1 624 70 47 23 75 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666 76 47 29 72 +QUAL 1 667 73 43 30 88 +QUAL 1 668 85 55 30 63 +QUAL 1 669 59 41 18 65 +QUAL 1 670 72 53 19 94 +QUAL 1 671 76 46 30 71 +QUAL 1 672 58 31 26 72 +QUAL 1 673 79 46 33 97 +QUAL 1 674 77 54 23 72 +QUAL 1 675 67 45 22 62 +QUAL 1 676 74 49 25 96 +QUAL 1 677 69 44 25 67 +QUAL 1 678 63 40 23 75 +QUAL 1 679 78 43 35 98 +QUAL 1 680 87 54 32 52 +QUAL 1 681 83 49 34 90 +QUAL 1 682 84 56 28 147 +QUAL 1 683 93 58 35 60 +QUAL 1 684 75 43 31 70 +QUAL 1 685 81 47 34 90 +QUAL 1 686 88 53 35 65 +QUAL 1 687 83 49 33 66 +QUAL 1 688 69 42 27 80 +QUAL 1 689 77 55 22 81 +QUAL 1 690 62 44 18 49 +QUAL 1 691 101 55 46 76 +QUAL 1 692 95 63 32 65 +QUAL 1 693 63 38 25 62 +QUAL 1 694 79 47 32 94 +QUAL 1 695 72 47 25 72 +QUAL 1 696 73 48 25 75 +QUAL 1 697 95 59 36 69 +QUAL 1 698 80 54 26 75 +QUAL 1 699 71 49 22 68 +QUAL 1 700 72 38 34 91 +QUAL 1 701 71 46 23 65 +QUAL 1 702 89 45 44 56 +QUAL 1 703 73 45 28 92 +QUAL 1 704 77 46 31 52 +QUAL 1 705 75 45 29 69 +QUAL 1 706 76 41 34 75 +QUAL 1 707 50 33 17 83 +QUAL 1 708 69 41 28 74 +QUAL 1 709 76 49 27 71 +QUAL 1 710 91 67 24 68 +QUAL 1 711 82 58 24 71 +QUAL 1 712 52 32 20 84 +QUAL 1 713 76 42 34 54 +QUAL 1 714 95 52 43 68 +QUAL 1 715 71 45 25 74 +QUAL 1 716 91 59 31 70 +QUAL 1 717 76 40 36 66 +QUAL 1 718 53 40 13 75 +QUAL 1 719 71 48 21 54 +QUAL 1 720 86 56 30 80 +QUAL 1 721 72 37 34 77 +QUAL 1 722 68 46 22 62 +QUAL 1 723 88 54 34 70 +QUAL 1 724 81 48 33 74 +QUAL 1 725 73 43 29 47 +QUAL 1 726 81 48 33 64 +QUAL 1 727 82 60 22 147 +QUAL 1 728 85 43 42 54 +QUAL 1 729 73 47 26 57 +QUAL 1 730 76 48 26 80 +QUAL 1 731 71 45 26 46 +QUAL 1 732 72 43 28 48 +QUAL 1 733 80 54 26 81 +QUAL 1 734 68 41 27 49 +QUAL 1 735 73 47 25 57 +QUAL 1 736 87 46 41 75 +QUAL 1 737 76 44 31 60 +QUAL 1 738 63 36 27 60 +QUAL 1 739 79 48 31 64 +QUAL 1 740 77 49 28 53 +QUAL 1 741 71 45 26 51 +QUAL 1 742 84 41 43 79 +QUAL 1 743 66 46 20 49 +QUAL 1 744 70 34 35 70 +QUAL 1 745 67 42 24 85 +QUAL 1 746 74 43 31 49 +QUAL 1 747 67 43 24 61 +QUAL 1 748 56 35 21 66 +QUAL 1 749 79 51 28 63 +QUAL 1 750 76 50 25 58 +QUAL 1 751 52 34 18 55 +QUAL 1 752 91 60 31 64 +QUAL 1 753 73 43 30 69 +QUAL 1 754 77 46 31 76 +QUAL 1 755 70 45 25 54 +QUAL 1 756 73 52 21 47 +QUAL 1 757 89 64 25 81 +QUAL 1 758 74 44 30 39 +QUAL 1 759 70 42 28 74 +QUAL 1 760 59 35 24 83 +QUAL 1 761 68 43 23 55 +QUAL 1 762 74 45 28 61 +QUAL 1 763 87 57 29 69 +QUAL 1 764 65 44 21 45 +QUAL 1 765 78 44 34 60 +QUAL 1 766 50 27 23 71 +QUAL 1 767 75 43 31 58 +QUAL 1 768 79 49 29 75 +QUAL 1 769 83 51 32 66 +QUAL 1 770 75 44 29 63 +QUAL 1 771 62 42 19 72 +QUAL 1 772 75 47 27 111 +QUAL 1 773 59 41 18 60 +QUAL 1 774 65 35 30 47 +QUAL 1 775 80 60 20 60 +QUAL 1 776 61 39 22 50 +QUAL 1 777 67 40 27 60 +QUAL 1 778 64 37 27 63 +QUAL 1 779 81 54 27 50 +QUAL 1 780 59 35 24 59 +QUAL 1 781 106 54 52 74 +QUAL 1 782 55 34 20 41 +QUAL 1 783 67 41 26 58 +QUAL 1 784 67 44 23 66 +QUAL 1 785 63 37 26 54 +QUAL 1 786 59 37 22 39 +QUAL 1 787 70 46 24 44 +QUAL 1 788 68 38 28 40 +QUAL 1 789 84 61 23 54 +QUAL 1 790 60 37 23 56 +QUAL 1 791 70 45 25 51 +QUAL 1 792 64 40 24 46 +QUAL 1 793 85 50 35 60 +QUAL 1 794 69 33 36 46 +QUAL 1 795 61 36 25 60 +QUAL 1 796 65 37 28 71 +QUAL 1 797 57 33 24 47 +QUAL 1 798 82 46 36 71 +QUAL 1 799 71 36 34 86 +QUAL 1 800 73 50 23 46 +QUAL 1 801 75 47 28 55 +QUAL 1 802 68 39 29 65 +QUAL 1 803 68 42 26 47 +QUAL 1 804 75 45 30 55 +QUAL 1 805 53 26 26 55 +QUAL 1 806 58 34 24 48 +QUAL 1 807 76 50 26 46 +QUAL 1 808 57 35 22 75 +QUAL 1 809 53 36 17 56 +QUAL 1 810 79 55 23 38 +QUAL 1 811 46 33 13 58 +QUAL 1 812 51 27 24 45 +QUAL 1 813 66 36 30 49 +QUAL 1 814 64 31 33 62 +QUAL 1 815 65 38 25 44 +QUAL 1 816 64 40 23 57 +QUAL 1 817 70 43 27 136 +QUAL 1 818 61 44 17 47 +QUAL 1 819 61 39 22 50 +QUAL 1 820 70 42 27 54 +QUAL 1 821 44 25 19 50 +QUAL 1 822 66 46 20 47 +QUAL 1 823 57 33 24 68 +QUAL 1 824 48 30 18 45 +QUAL 1 825 64 44 20 52 +QUAL 1 826 88 46 41 59 +QUAL 1 827 50 32 18 42 +QUAL 1 828 52 36 16 53 +QUAL 1 829 56 37 19 58 +QUAL 1 830 62 47 15 53 +QUAL 1 831 51 30 21 46 +QUAL 1 832 60 35 23 69 +QUAL 1 833 47 31 16 48 +QUAL 1 834 55 35 20 52 +QUAL 1 835 62 36 26 68 +QUAL 1 836 60 32 28 39 +QUAL 1 837 62 39 23 49 +QUAL 1 838 69 42 27 56 +QUAL 1 839 44 26 18 43 +QUAL 1 840 69 45 24 45 +QUAL 1 841 64 47 17 50 +QUAL 1 842 52 33 19 43 +QUAL 1 843 55 38 17 66 +QUAL 1 844 71 39 31 66 +QUAL 1 845 50 30 20 45 +QUAL 1 846 57 31 26 60 +QUAL 1 847 73 42 31 61 +QUAL 1 848 49 28 21 41 +QUAL 1 849 47 26 21 43 +QUAL 1 850 64 34 28 54 +QUAL 1 851 49 21 27 37 +QUAL 1 852 47 28 19 53 +QUAL 1 853 56 41 15 53 +QUAL 1 854 59 31 28 40 +QUAL 1 855 56 36 19 50 +QUAL 1 856 63 36 26 74 +QUAL 1 857 43 25 18 28 +QUAL 1 858 48 25 23 51 +QUAL 1 859 47 35 12 62 +QUAL 1 860 54 32 22 40 +QUAL 1 861 54 34 20 49 +QUAL 1 862 47 32 15 121 +QUAL 1 863 39 23 16 47 +QUAL 1 864 48 35 13 32 +QUAL 1 865 53 32 21 57 +QUAL 1 866 46 32 13 55 +QUAL 1 867 51 34 17 37 +QUAL 1 868 66 39 27 73 +QUAL 1 869 46 28 18 38 +QUAL 1 870 62 37 25 50 +QUAL 1 871 72 42 30 57 +QUAL 1 872 51 35 16 43 +QUAL 1 873 48 33 15 47 +QUAL 1 874 53 37 15 57 +QUAL 1 875 38 25 13 45 +QUAL 1 876 48 31 17 41 +QUAL 1 877 45 23 21 44 +QUAL 1 878 59 34 25 46 +QUAL 1 879 59 38 20 47 +QUAL 1 880 58 30 28 73 +QUAL 1 881 39 23 16 56 +QUAL 1 882 51 32 18 59 +QUAL 1 883 48 32 16 52 +QUAL 1 884 42 28 14 37 +QUAL 1 885 50 29 21 48 +QUAL 1 886 50 31 19 41 +QUAL 1 887 45 25 19 47 +QUAL 1 888 47 26 21 46 +QUAL 1 889 56 27 29 52 +QUAL 1 890 53 32 21 32 +QUAL 1 891 61 40 21 42 +QUAL 1 892 50 29 20 50 +QUAL 1 893 48 31 17 39 +QUAL 1 894 53 24 29 45 +QUAL 1 895 45 35 10 37 +QUAL 1 896 44 30 14 32 +QUAL 1 897 50 33 17 38 +QUAL 1 898 53 35 18 50 +QUAL 1 899 51 39 11 34 +QUAL 1 900 57 35 22 43 +QUAL 1 901 39 25 13 47 +QUAL 1 902 50 32 18 39 +QUAL 1 903 54 29 25 48 +QUAL 1 904 43 27 16 65 +QUAL 1 905 46 30 16 40 +QUAL 1 906 53 30 23 48 +QUAL 1 907 60 35 25 104 +QUAL 1 908 38 27 11 34 +QUAL 1 909 51 33 17 42 +QUAL 1 910 46 28 18 42 +QUAL 1 911 41 26 15 37 +QUAL 1 912 38 20 18 36 +QUAL 1 913 35 19 16 59 +QUAL 1 914 40 25 14 32 +QUAL 1 915 42 28 13 32 +QUAL 1 916 69 47 22 41 +QUAL 1 917 42 33 9 37 +QUAL 1 918 46 31 14 37 +QUAL 1 919 54 29 24 37 +QUAL 1 920 38 24 14 30 +QUAL 1 921 37 24 13 33 +QUAL 1 922 43 23 19 40 +QUAL 1 923 49 25 23 35 +QUAL 1 924 36 26 10 46 +QUAL 1 925 49 33 16 37 +QUAL 1 926 53 38 15 25 +QUAL 1 927 55 38 16 44 +QUAL 1 928 42 27 15 44 +QUAL 1 929 40 24 15 33 +QUAL 1 930 35 19 16 45 +QUAL 1 931 44 23 21 33 +QUAL 1 932 39 25 14 39 +QUAL 1 933 52 34 18 31 +QUAL 1 934 57 34 23 42 +QUAL 1 935 32 19 13 21 +QUAL 1 936 45 24 21 38 +QUAL 1 937 50 36 13 32 +QUAL 1 938 45 29 16 37 +QUAL 1 939 43 25 18 34 +QUAL 1 940 48 31 17 42 +QUAL 1 941 26 16 10 39 +QUAL 1 942 44 24 19 27 +QUAL 1 943 42 29 12 46 +QUAL 1 944 48 28 20 30 +QUAL 1 945 47 28 19 42 +QUAL 1 946 36 23 13 45 +QUAL 1 947 60 40 19 42 +QUAL 1 948 49 21 28 37 +QUAL 1 949 30 17 13 40 +QUAL 1 950 37 25 12 36 +QUAL 1 951 39 28 11 54 +QUAL 1 952 38 22 15 74 +QUAL 1 953 40 25 15 36 +QUAL 1 954 39 25 14 53 +QUAL 1 955 35 19 16 37 +QUAL 1 956 35 25 10 27 +QUAL 1 957 38 27 10 29 +QUAL 1 958 47 30 17 44 +QUAL 1 959 36 23 12 34 +QUAL 1 960 43 23 20 33 +QUAL 1 961 42 24 17 44 +QUAL 1 962 50 36 14 32 +QUAL 1 963 44 26 17 36 +QUAL 1 964 39 27 12 32 +QUAL 1 965 38 23 15 32 +QUAL 1 966 42 27 15 44 +QUAL 1 967 36 22 14 31 +QUAL 1 968 45 27 18 27 +QUAL 1 969 39 26 13 39 +QUAL 1 970 31 19 12 39 +QUAL 1 971 40 23 17 20 +QUAL 1 972 36 18 17 40 +QUAL 1 973 35 19 16 32 +QUAL 1 974 36 19 17 27 +QUAL 1 975 49 26 23 31 +QUAL 1 976 31 17 13 28 +QUAL 1 977 24 15 9 26 +QUAL 1 978 33 15 18 46 +QUAL 1 979 37 24 13 30 +QUAL 1 980 30 19 11 35 +QUAL 1 981 38 22 16 37 +QUAL 1 982 45 30 15 38 +QUAL 1 983 44 26 17 36 +QUAL 1 984 40 26 13 36 +QUAL 1 985 32 15 17 30 +QUAL 1 986 18 11 6 26 +QUAL 1 987 34 20 14 29 +QUAL 1 988 27 16 11 47 +QUAL 1 989 32 21 10 35 +QUAL 1 990 39 25 13 32 +QUAL 1 991 33 22 11 30 +QUAL 1 992 37 22 15 25 +QUAL 1 993 52 32 19 50 +QUAL 1 994 34 21 13 33 +QUAL 1 995 30 21 9 27 +QUAL 1 996 35 24 10 47 +QUAL 1 997 35 20 15 74 +QUAL 1 998 20315 11927 8246 14996 +# IDD, InDel distribution: +# IDD [2]id [3]length (deletions negative) [4]count +IDD 0 -60 270 +IDD 0 -59 10 +IDD 0 -58 15 +IDD 0 -57 9 +IDD 0 -56 22 +IDD 0 -55 14 +IDD 0 -54 18 +IDD 0 -53 11 +IDD 0 -52 18 +IDD 0 -51 12 +IDD 0 -50 72 +IDD 0 -49 67 +IDD 0 -48 94 +IDD 0 -47 49 +IDD 0 -46 82 +IDD 0 -45 53 +IDD 0 -44 102 +IDD 0 -43 60 +IDD 0 -42 120 +IDD 0 -41 77 +IDD 0 -40 213 +IDD 0 -39 84 +IDD 0 -38 175 +IDD 0 -37 114 +IDD 0 -36 246 +IDD 0 -35 124 +IDD 0 -34 223 +IDD 0 -33 149 +IDD 0 -32 377 +IDD 0 -31 188 +IDD 0 -30 478 +IDD 0 -29 215 +IDD 0 -28 580 +IDD 0 -27 293 +IDD 0 -26 545 +IDD 0 -25 434 +IDD 0 -24 1017 +IDD 0 -23 406 +IDD 0 -22 887 +IDD 0 -21 572 +IDD 0 -20 1725 +IDD 0 -19 710 +IDD 0 -18 1568 +IDD 0 -17 844 +IDD 0 -16 2673 +IDD 0 -15 1712 +IDD 0 -14 2622 +IDD 0 -13 1559 +IDD 0 -12 5760 +IDD 0 -11 2062 +IDD 0 -10 5847 +IDD 0 -9 3272 +IDD 0 -8 10539 +IDD 0 -7 4145 +IDD 0 -6 13029 +IDD 0 -5 12425 +IDD 0 -4 43999 +IDD 0 -3 29979 +IDD 0 -2 79663 +IDD 0 -1 211224 +IDD 0 1 213461 +IDD 0 2 77400 +IDD 0 3 27382 +IDD 0 4 40992 +IDD 0 5 11002 +IDD 0 6 11805 +IDD 0 7 3415 +IDD 0 8 9529 +IDD 0 9 2693 +IDD 0 10 4717 +IDD 0 11 1486 +IDD 0 12 4731 +IDD 0 13 1025 +IDD 0 14 1866 +IDD 0 15 1265 +IDD 0 16 2099 +IDD 0 17 616 +IDD 0 18 1040 +IDD 0 19 481 +IDD 0 20 1228 +IDD 0 21 417 +IDD 0 22 510 +IDD 0 23 279 +IDD 0 24 694 +IDD 0 25 298 +IDD 0 26 337 +IDD 0 27 217 +IDD 0 28 330 +IDD 0 29 154 +IDD 0 30 277 +IDD 0 31 131 +IDD 0 32 231 +IDD 0 33 106 +IDD 0 34 121 +IDD 0 35 100 +IDD 0 36 141 +IDD 0 37 96 +IDD 0 38 98 +IDD 0 39 69 +IDD 0 40 113 +IDD 0 41 64 +IDD 0 42 82 +IDD 0 43 42 +IDD 0 44 54 +IDD 0 45 48 +IDD 0 46 54 +IDD 0 47 42 +IDD 0 48 59 +IDD 0 49 38 +IDD 0 50 47 +IDD 0 51 18 +IDD 0 52 27 +IDD 0 53 11 +IDD 0 54 27 +IDD 0 55 12 +IDD 0 56 29 +IDD 0 57 12 +IDD 0 58 15 +IDD 0 59 9 +IDD 0 60 338 +IDD 1 -60 1636 +IDD 1 -59 25 +IDD 1 -58 52 +IDD 1 -57 46 +IDD 1 -56 83 +IDD 1 -55 46 +IDD 1 -54 63 +IDD 1 -53 40 +IDD 1 -52 96 +IDD 1 -51 60 +IDD 1 -50 71 +IDD 1 -49 83 +IDD 1 -48 95 +IDD 1 -47 40 +IDD 1 -46 56 +IDD 1 -45 52 +IDD 1 -44 85 +IDD 1 -43 58 +IDD 1 -42 86 +IDD 1 -41 47 +IDD 1 -40 157 +IDD 1 -39 80 +IDD 1 -38 93 +IDD 1 -37 74 +IDD 1 -36 173 +IDD 1 -35 111 +IDD 1 -34 145 +IDD 1 -33 105 +IDD 1 -32 240 +IDD 1 -31 109 +IDD 1 -30 242 +IDD 1 -29 127 +IDD 1 -28 307 +IDD 1 -27 166 +IDD 1 -26 312 +IDD 1 -25 211 +IDD 1 -24 510 +IDD 1 -23 205 +IDD 1 -22 407 +IDD 1 -21 250 +IDD 1 -20 715 +IDD 1 -19 272 +IDD 1 -18 632 +IDD 1 -17 334 +IDD 1 -16 1093 +IDD 1 -15 597 +IDD 1 -14 886 +IDD 1 -13 503 +IDD 1 -12 1805 +IDD 1 -11 695 +IDD 1 -10 1697 +IDD 1 -9 961 +IDD 1 -8 2970 +IDD 1 -7 1267 +IDD 1 -6 3279 +IDD 1 -5 2215 +IDD 1 -4 6160 +IDD 1 -3 4442 +IDD 1 -2 11182 +IDD 1 -1 17759 +IDD 1 1 20283 +IDD 1 2 11734 +IDD 1 3 4605 +IDD 1 4 6473 +IDD 1 5 2406 +IDD 1 6 3616 +IDD 1 7 1404 +IDD 1 8 3622 +IDD 1 9 1106 +IDD 1 10 2273 +IDD 1 11 830 +IDD 1 12 2276 +IDD 1 13 613 +IDD 1 14 1206 +IDD 1 15 682 +IDD 1 16 1333 +IDD 1 17 354 +IDD 1 18 891 +IDD 1 19 285 +IDD 1 20 1028 +IDD 1 21 265 +IDD 1 22 550 +IDD 1 23 261 +IDD 1 24 663 +IDD 1 25 252 +IDD 1 26 373 +IDD 1 27 225 +IDD 1 28 467 +IDD 1 29 158 +IDD 1 30 336 +IDD 1 31 145 +IDD 1 32 313 +IDD 1 33 125 +IDD 1 34 183 +IDD 1 35 140 +IDD 1 36 219 +IDD 1 37 88 +IDD 1 38 120 +IDD 1 39 90 +IDD 1 40 192 +IDD 1 41 73 +IDD 1 42 101 +IDD 1 43 70 +IDD 1 44 108 +IDD 1 45 64 +IDD 1 46 78 +IDD 1 47 62 +IDD 1 48 115 +IDD 1 49 69 +IDD 1 50 88 +IDD 1 51 54 +IDD 1 52 97 +IDD 1 53 63 +IDD 1 54 84 +IDD 1 55 56 +IDD 1 56 70 +IDD 1 57 56 +IDD 1 58 76 +IDD 1 59 45 +IDD 1 60 1909 +# ST, Substitution types: +# ST [2]id [3]type [4]count +ST 0 A>C 159748 +ST 0 A>G 626463 +ST 0 A>T 139745 +ST 0 C>A 164508 +ST 0 C>G 166313 +ST 0 C>T 655172 +ST 0 G>A 656529 +ST 0 G>C 166516 +ST 0 G>T 165243 +ST 0 T>A 139268 +ST 0 T>C 626583 +ST 0 T>G 159950 +ST 1 A>C 4930 +ST 1 A>G 12526 +ST 1 A>T 5061 +ST 1 C>A 6002 +ST 1 C>G 4937 +ST 1 C>T 15916 +ST 1 G>A 15601 +ST 1 G>C 5370 +ST 1 G>T 5848 +ST 1 T>A 5838 +ST 1 T>C 12731 +ST 1 T>G 4612 +# DP, Depth distribution +# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%) +DP 0 0 36 0.000777 3 0.000065 +DP 0 1 396 0.008547 169 0.003648 +DP 0 2 1145 0.024714 621 0.013403 +DP 0 3 3564 0.076927 2707 0.058427 +DP 0 4 3986 0.086036 2944 0.063542 +DP 0 5 4633 0.100001 3211 0.069305 +DP 0 6 4965 0.107167 3461 0.074700 +DP 0 7 5552 0.119837 3793 0.081866 +DP 0 8 6218 0.134212 4252 0.091773 +DP 0 9 6906 0.149062 4620 0.099716 +DP 0 10 7514 0.162186 5234 0.112968 +DP 0 11 8213 0.177273 5722 0.123501 +DP 0 12 9087 0.196138 6500 0.140293 +DP 0 13 9682 0.208981 7020 0.151516 +DP 0 14 10561 0.227954 7736 0.166970 +DP 0 15 11444 0.247013 8514 0.183762 +DP 0 16 12414 0.267950 9245 0.199539 +DP 0 17 12954 0.279606 9759 0.210633 +DP 0 18 14281 0.308248 10769 0.232433 +DP 0 19 15288 0.329984 11700 0.252527 +DP 0 20 16639 0.359144 12559 0.271067 +DP 0 21 18055 0.389708 13954 0.301176 +DP 0 22 19448 0.419775 15445 0.333357 +DP 0 23 20946 0.452109 16743 0.361373 +DP 0 24 23472 0.506631 19141 0.413130 +DP 0 25 26452 0.570953 21402 0.461930 +DP 0 26 29724 0.641577 24997 0.539523 +DP 0 27 34312 0.740607 28816 0.621950 +DP 0 28 39397 0.850364 34079 0.735544 +DP 0 29 45714 0.986713 39641 0.855591 +DP 0 30 53199 1.148273 47147 1.017597 +DP 0 31 61474 1.326885 55429 1.196352 +DP 0 32 71870 1.551277 65972 1.423907 +DP 0 33 83218 1.796218 77339 1.669246 +DP 0 34 95908 2.070125 90464 1.952530 +DP 0 35 108737 2.347033 103687 2.237928 +DP 0 36 121779 2.628538 117667 2.539666 +DP 0 37 135262 2.919562 132247 2.854353 +DP 0 38 148227 3.199404 145742 3.145622 +DP 0 39 160701 3.468649 158984 3.431431 +DP 0 40 171234 3.695999 171762 3.707225 +DP 0 41 180863 3.903836 181727 3.922305 +DP 0 42 187287 4.042495 189707 4.094541 +DP 0 43 192197 4.148475 195327 4.215840 +DP 0 44 194487 4.197903 198356 4.281217 +DP 0 45 193851 4.184175 199348 4.302627 +DP 0 46 190865 4.119724 197484 4.262396 +DP 0 47 185644 4.007031 192570 4.156334 +DP 0 48 177527 3.831830 185287 3.999142 +DP 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496 1 0.000439 1 0.000439 +DP 1 498 0 0.000000 1 0.000439 +DP 1 >500 561 0.246181 595 0.260947 +# PSC, Per-sample counts +# PSC [2]id [3]sample [4]nRefHom [5]nNonRefHom [6]nHets [7]nTransitions [8]nTransversions [9]nIndels [10]average depth [11]nSingletons +PSC 0 testvcf 0 1483533 2341091 2563709 1259694 812503 44.6 4632959 +PSC 1 testvcf 0 8189 91085 56562 42371 129064 47.4 227887 +# PSI, Per-Sample Indels +# PSI [2]id [3]sample [4]in-frame [5]out-frame [6]not applicable [7]out/(in+out) ratio [8]nHets [9]nAA +PSI 0 testvcf 0 0 0 0.00 507357 305146 +PSI 1 testvcf 0 0 0 0.00 99723 29341 +# HWE +# HWE [2]id [3]1st ALT allele frequency [4]Number of observations [5]25th percentile [6]median [7]75th percentile +HWE 0 0.000000 2844280 0.990000 0.990000 0.990000 +HWE 0 99.000000 1788679 0.000000 0.000000 0.000000 +HWE 1 0.000000 190357 0.990000 0.990000 0.990000 +HWE 1 99.000000 37530 0.000000 0.000000 0.000000