Fig. 2
Schematic overview and characteristics of human genome-aligned mouse allele (HAMA). a Definition of HAMA and their allele frequency. Hf is defined as x/d, where d is the total depth of given position, and x is the depth of all allele from mouse reads. b Common and Strain-specific HAMA. c Types of HAMA alleles. HAMA alleles consist of 87.37% homozygous SNVs, 7.56% heterozygous SNVs, and 5.07% indels. If any of the five mouse samples were reported as heterozygous SNVs, we counted as heterozygous SNVs. d Example of genomic regions that contains high-risk HAMAs (50% contamination ratio, TP53, exons 1–5). The coverage of human reads colored in yellow and mouse reads in blue. Red arrows indicate the genomic regions where the coverage of mouse reads dominates that of human reads. e Distributions of Hf for all HAMA sites in four different global contamination levels (5%, 10%, 20%, and 50%). Median Hf is denoted by dotted lines. f Estimation results of all in silico contaminated dataset based on the linear regression of median Hf. Red dotted line indicates the perfect estimation line