Additional file 3 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

Additional file 3 This table summarizes additional benchmark metrics of the haplotype solution of the NA12878 genome in comparison to the haplotype phase derived from parental genome sequencing. The parental haplotype data used for comparison include the reference haplotype data released by the Genome-In-A-Bottle consortium (“trio phase”), and phased haplotypes derived from de novo diploid assembly of the NA12878 genome (“dip assembly”) using PacBio CCS reads of the NA12878 genome and short reads of the parental genomes. See Table 1 for more details about the reference haplotype data. In the 1st Tab, each row summarizes the following metrics about the haplotype solution of each chromosome (column 1): phased sites from de novo diploid assembly (column 2), phased sites in the GIAB release (column 3), phased sites in the final unfiltered haplotype solution from mLinker (column 4), phased genotypes in the mLinker solution that are in agreement with the GIAB data (column 5), mLinker phased genotypes in discordance with the GIAB data (column 6), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 7), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 8), phased sites in the final filtered haplotype solution from mLinker (column 9), mLinker phased genotypes in agreement with the GIAB data (column 10), mLinker phased genotypes in discordance with the GIAB data (column 11), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 12), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 13). The 2nd Tab reports results of the comparison of mLinker-phased genotypes on each parental chromosome with parent-specific sequences derived from the short-read sequencing data of parental genomes. For details about this comparison, see Additional file 1:Comparison of phased variant genotypes with parent-specific k-mer’s.