Figure S4.

Comparison of small variant calls to the phase 3 call set, related to Figure 3

(A) Length of INDELs in the high-coverage as compared to the phase 3 call sets. (B) Number of true positive (TP), false positive (FP), and false negative (FN) SNVs and INDELs in the high-coverage vs. phase 3 call set, stratified by easy and difficult regions of the genome (GIAB v3.3.2 high confidence regions only). (C) Comparison of allele frequencies in the high-coverage vs. the phase 3 call set across shared loci, stratified by variant type and regions of the genome. r: Pearson correlation coefficient. Number of false positive (FP), true positive (TP), and unassessed (NA; sites outside of the GIAB v3.3.2 high confidence regions of the genome) predicted functional SNVs (D) and INDELs (E) in sample NA12878, defined based on the comparison against the GIAB NA12878 truth set v3.3.2. There were no stop-loss INDELs in sample NA12878 hence no plot for that category in E. See also Figures 3G and 3H (bottom row). Panels A, C, D, E: chr1-22; panel B: chr1-22 and X