The comparisons of KIR gene copy number results of T1K and SKIRT. (A) The precision and recall rate of copy numbers determined by T1K-annotate and T1K-genotype as compared with SKIRT in 26 HPRC genomes. The gene copy numbers detected by T1K-annotate and T1K-genotype are compared separately with the results of SKIRT as the ground truth. T1K-annotate exhibits perfect precision and recall of 100% in almost all KIR genes, except for a 98% recall rate for both KIR2DS4 and KIR3DL2 and a 98% precision rate for KIR3DP1. Nevertheless, T1K-genotype shows recall rates of <90% for 13 out of 17 genes. (B) The agreement between T1K-annotate and SKIRT for the allele annotation of 26 HPRC genomes. Each allele annotation of T1K is compared with the results of SKIRT at two resolution levels: three digit and five digit. If a candidate allele annotated by T1K matches that of SKIRT in the same haplotype, it is marked as one in agreement. If T1K gives one or multiple candidate alleles with differences only in the sixth and seventh digits compared with the one assigned by SKIRT, the agreement was assigned on the five-digit level. If the first three digits were the same but the fourth and fifth digits were different, the agreement was assigned on three-digit level.
