Figure 2

Detection of de novo SNVs and INDELs by WGS of mouse GS and mGS cell lines. (a and b) Mutation rates of SNVs (a) and INDELs (b) in GS and mGS cells. The values are the estimated numbers of de novo SNVs (a) and INDELs (b) detected by the comparative analyses of WGS data of each subclone and corresponding parental cultures of GS and mGS cells divided by the effective diploid genome length in base pairs and by the number of population doublings. To derive these estimated values, a Gauss model was fitted to allele frequency distributions of each sample after trimming de novo mutations with low allele frequencies (see Materials and methods). Data were obtained from two independent experiments (exp1 and exp2). One mGS subclone (subclone2 in exp1) was omitted as an outlier from our analyses. The red bars represent mean ± SD. (c) Chromosomal distribution of de novo SNVs in GS and mGS cells. Data from each subclone in exp1 and exp2 were combined for GS cells (orange vertical lines) and mGS cells (blue vertical lines), respectively. The X and Y chromosomes were excluded from our analyses, as the sequence read coverages on these chromosomes were variable due to the abundance of repeat sequences. (d) Number of de novo SNVs per chromosome normalized by 100 Mbp. Colored dots represent each subclone of GS (top) and mGS (bottom), with the vertical bars showing mean ± SD. (e) Chromosomal distribution of de novo INDELs in GS and mGS cells with the data presented similarly in (c). (f) Base-pair length of de novo INDELs [insertions on the right (> 0) and deletions on the left (< 0)] of GS cells (orange) and mGS cells (blue), with the data from each subclone in exp1 and exp2 combined.