Fig. 2: Replication rate is associated with reported quality metrics.

a Proportion of SVs and STRs that were non-reference (green) in at least one of the iPSCORE MZ twin pairs or HipSci fibroblast–iPSC pairs prior to filtering. b Replication rate of variants before and after filtering and deduplicating within caller; Genome STRiP and SpeedSeq abbreviated in figure as GS and SS respectively. c Replication rate in MZ twins versus the number of total SpeedSeq (LUMPY) sites remaining that pass criteria when filtering variants to different thresholds for MSQ score (indicated by color). d Replication rate versus the number of total Genome STRiP sites remaining that pass criteria when filtering variants to different thresholds for GSCNQUAL score (indicated by color). e Replication rate in MZ twins for MELT sites that pass criteria when filtering variants under suggested hard site filters (left). Pink represents the result of filtering using all four exclusion criteria (rSD, s25, hDP, lc; see Methods). The number of total sites remaining that passed criteria is shown at right.