Mapping efficiency for HLA-DRB1 genes. Sample SRR360148 is heterozygote with alleles DRB1*01:01 and DRB1*15:01. Sample SRR359103 is heterozygote with alleles DRB1*03:01 and DRB1*07:01. (a) Difference in the number of reads captured on the exon 2 region for sample SRR360148. Clearly a multiple allele-based mapping panel that contains eight different alleles of HLA-DRB1 outperforms a single reference hg19*15:01:01:01 (that is, PGF). (b) The total number of reads captured using hg19*15:01:01:01 as reference only versus a multiple allele-based reference panel for samples SRR360148 and SRR359103. Using one mapping reference would lose quite a number of short reads.