smn1_cn: copy number of SMN1, anullcall indicates that Paraphase finds only one haplotype but depth does not unambiguously support a copy number of one or two.smn2_cn: copy number of SMN2, anullcall indicates that Paraphase finds only one haplotype but depth does not unambiguously support a copy number of one or two.smn2_del78_cn: copy number of SMN2Δ7–8 (SMN2 with a deletion of Exon7-8)smn1_read_number: number of reads containing c.840Csmn2_read_number: number of reads containing c.840Tsmn2_del78_read_number: number of reads containing the known deletion of Exon7-8 on SMN2smn1_haplotypes: phased SMN1 haplotypessmn2_haplotypes: phased SMN2 haplotypessmn2_del78_haplotypes: phased SMN2Δ7–8 haplotypestwo_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.haplotype_details: lists information about each haplotypeboundary: The boundary of the region that is resolved on the haplotype. This is useful when a haplotype is only partially phased.haplogroup: The haplogroup that the haplotype is assigned to. For more information on haplogroups, please refer to our paper.
We can visualize the haplotypes by loading the Paraphase output bam file into IGV and grouping reads by the HP tag (also color alignments by YC tag).
In this example, there are two copies of SMN1, one copy of SMN2Δ7–8, and one copy of intact SMN2. All reads are realigned to SMN1. Polymorphic sites used for phasing/assembling haplotypes are shown in the top panel. The Unassigned category contains reads that carry bases that do not support any haplotypes (this could be due to sequencing errors or partially phased haplotypes).
In this example, there are three copies of SMN1 and one copy of SMN2. Reads in blue are uniquely assigned to a haplotype. Reads in gray are consistent with more than one possible haplotype (this happens when those haplotypes are identical over a region). Here smn1hap1, smn1hap3 and smn2hap1 are identical from the region upstream of SMN1 all the way to halfway into Intron 1 (their sequences are identical at the first two variant sites). When there are several possible haplotypes consistent with a read, the read is randomly assigned to a haplotype and colored in gray.
In this example, Paraphase assembles one SMN1 haplotype and two SMN2 haplotypes. The depth of smn1hap1 suggests that it is present in two copies, so Paraphase infers that there are two copies of SMN1 (their haplotype sequences are identical). Note that the majority of the Unassigned reads are "unassigned" because they do not overlap any polymorphic site.
For more examples on SMN1/SMN2, IGV session files for 107 Coriell samples can be downloaded from here.