Fig. 2

Detection of SNPs, indels, and CNVs in the SW480 cell line using MGA-Seq. a Comparison of the numbers of SNPs and indels (< 50 bp, include insertions and deletions) identified by WGS, MGA-Seq, and Hi-C. b Overlap of the SNPs and indels between MGA-Seq, WGS, and Hi-C. c Scatter plot of sequencing depth and coverage for each chromosome. Blue points represent MGA-Seq, yellow points represent WGS, and green points represent Hi-C. X-axis represents coverage, and Y-axis represents sequencing depth. The five acrocentric chromosomes (13, 14, 15, 21, and 22) possess extensive repetitive regions within their short arms, leading to relatively lower coverage in chromosome mapping, as indicated in the figure. d Comparison of log₂ copy ratios calculated by BIC-SEQ2. The CNV segmentation is plotted in red with log₂ copy ratio, and the black dot represents the log₂ copy ratio per bin. e Comparison of the CNVs on chromosome 3 identified by Hi-C, MGA-Seq, and WGS. f Statistics of the number and size distribution of CNVs identified by Hi-C, MGA-Seq, and WGS. g Consistency of the CNV segments (categorized by size) detected by Hi-C and WGS. Overall, Hi-C cannot detect CNV with length less than 20 Mb. h Consistency of the CNV segments detected by MGA-Seq and WGS. The number and size distribution of CNV segments detected by MGA-Seq and WGS are highly consistent, especially for micro-CNVs (< 1 Mb)