MHC variant comparison of the pangenome aligners. The top row, from left to right, displays bar plots of the F1, precision, and recall scores for the SNPs and indels called by DeepVariant from the linear MHC reference alignments. The middle row displays the same metrics for the pan-MHC reference alignments. The bottom row, from left to right, displays the average percentage differences for the F1, precision, and recall metrics between the pan-MHC and linear MHC reference alignments. The aligners are indicated by the color of the bar with green corresponding to Moni-align, blue corresponding to vg map, and orange corresponding to vg giraffe. The error bars are the standard deviations. Note that the x-axis categories have a type subtype notation. The two types are SNP and indel. Indels are further categorized as insertions (I) and deletions (D). The subtypes are as follows: (asterisk) all subtypes, (1_5) 1–5 bp, (6_15) 6–15 bp, and (16_PLUS) ≥16 bp.
