Fig. 8

Pairwise comparisons of haplotype data between replicates. For each sample, replicate libraries were analyzed through pairwise comparisons. Single nucleotide polymorphisms (SNPs) were filtered with the same criteria as used in Fig. 6: 1) Each SNP must have a PASS in the “varFilter” field. 2) The “wellCount” field should be equal to six or greater for both variant and reference calls. 3) The “SharedWellCount” field must be less than or equal to 0.25X (“MinExclusiveWellCountInThisLocus” + “SharedWellCount”). In addition, overlapping blocks must contain at least ten SNPs and only pairwise comparisons between 1 million or more SNPs were analyzed. This final criterion reduced the number of pairwise comparisons to 35 and the number of participant samples to 12. This filter was applied to remove Long Fragment Read (LFR) libraries that were intentionally made with low coverage and thus have sparse haplotype coverage. Switch discordances were calculated by comparing the phase of heterozygous SNPs in completely overlapping blocks between replicate samples. a Short switch discordance rates were calculated by dividing the total number of discordant SNPs by the total number of phased SNPs in the compared blocks. Long switch discordance rates were calculated by dividing the total number of long switch events by the total number of phased SNPs in the compared blocks. Individual pairwise comparisons are represented by small blue dots on the plot and the average of all 35 comparisons is represented by the large red dot. b The fraction of total blocks with no errors (red dotted line), with one short (black solid line) or long (block dashed line) switch discordance, two to three short (solid grey line) or long (dashed grey line) switch discordances, or four or more short (solid light grey line) or long (dashed light grey line) were plotted against the block length in base pairs (bp). The vast majority of compared blocks (~86 %) have no discordances. Of those blocks that are discordant, very few have more than one short or long switch