Fig. 5

Genotyping 100 diverse chickens. A, B Counts in millions of common and different SNVs (A) and indels (B) found by genotyping pipelines using giraffe vs. minimap as the aligner. Only variants with a quality score of at least 10 are considered. C, D Concordance distributions for SNVs (C) and indels (D) detected by both genotyping methods with QUAL ≥ 10. E Mean fractions per sample of mapped reads containing the alternate allele at putative heterozygous sites show that giraffe alignments contain less reference bias for every chicken, as they deviate less from the expected value of 0.5. Sample information in Additional file 3: Supplementary Table 2 and full plot for all 100 chickens in Additional file 2: Supplementary Fig. S6. F Genotyping 100 chickens at the K locus reproduces previous results finding that although most chickens with the late feathering allele (LF) also have an ev21 insertion at the K locus (ev21+), some chickens have the late feathering allele without an ev21 insertion