Additional file 4 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

Additional file 4 This table contains multiple tabs. Tab 1 reports results from the comparison of the mLinker haplotype solution of the RPE-1 genome generated from 60 × linked-reads and Hi-C sequencing data to the reference haplotype data derived from sequencing of monosomic chromosomes. Tabs 2-5 report results from the comparison of the mLinker haplotype resolution generated from downsampled linked-reads and Hi-C data. Tab 6 reports benchmark metrics of the mLinker haplotype solution generated from 11 × PacBio HiFi data and Hi-C data. In Tab 1, the comparison is performed on both the scaffold haplotype solution and the final haplotype solution filtered by haplotype linkage. In Tabs 2-5, the comparison is only performed on the scaffold haplotype solution. For each mLinker solution in Tabs 1-5, we report results from the comparison of phased genotypes at all phased variant sites (“No filter”), at phased sites not in centromeric/acrocentric regions (“Excluding centromere”), and at phased sites also passing the allele fraction filter from single-cell data (“allele filter from single-cell data”). In Tab 6, we report results from two separate calculations, the first using all variants as input, the second using only high-quality variants (sites that pass the linkage filter in the mLinker final haplotype solution derived from linked-reads and Hi-C data). The comparison in Tab 6 is only performed on high-quality variants.