Extended Data Fig. 5: A gene conversion in chromosome 2 A of individual G4-4.

a, Circos map showing all LOH regions in chromosome 2 A of individual G4-4. I, LOH region. II, LOH site number (Log2). III, SNP number (Log2). IV, read depth of SNP sites. The window size in II-IV is 200 kb. Red and blue bricks indicate gene conversion and gene deletion respectively. The orange and green lines in IV indicate the sequencing depth of 50× and 33× respectively. b, Phased haplotype blocks at the gene conversion boundary in a. The same region of individual G4-2 is shown as a control without gene conversion. Red bases, homozygous converted sites which resulted in LOH in this region. Green bases, heterozygous converted sites where the donor allele was minor allele. Blue bases, heterozygous sites where the donor allele had the same base as the recipient allele. Black bases with grey shadowed, heterozygous sites outside the converted region. Minor allele read frequencies (MAF) and depths of SNP sites in individual G4-4 are shown on the right panel. The total reads depth of this LOH region is consistent with non-LOH region, which is different from the LOH region caused by gene deletion. MAF of LOH sites equals to zero while others close to 1/3.