total_cn: total copy number of STRC and STRCP1gene_cn: copy number of the gene of interest, i.e. STRCtwo_copy_haplotypes: haplotypes that are present in two copies based on depth. This happens when (in a small number of cases) two haplotypes are identical and we infer that there exist two of them instead of one by checking the read depth.
To visualize phased haplotypes, load the output bam file in IGV, group reads by the HP tag and color alignments by YC tag. Reads are realigned to STRC.
Reads in blue are confidently consistent with a single haplotype. Reads in gray are either unassigned or consistent with more than one possible haplotype. When two haplotypes are identical over a region, there can be more than one haplotype consistent with a read, and the read is randomly assigned to a haplotype and colored in gray.
This example has two copies of STRC and two copies of STRCP1.