Fig. 2

Visualization of reads aligned to MHC class I alleles using BWA-MEM. Obtaining new class I alleles from RNA-Seq data by successive BWA-MEM/cap3 runs (DinoMfRS) using animal 01 and allele LfL2003 as an example. Caption of BWA-MEM alignment results from the initial (top: alignment of the RNA-Seq reads to the reference allele N*06:01, the range from nt 256 to 264, which is different from all known sheep alleles, is indicated by a red line) and final (bottom: alignment against the new allele LfL2003) BWA-MEM run. Identity to reference is shown in gray, differences are shown in color (G—blue, A—yellow, T—red, C—green)