Figure 4
From: Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
Read depth and SNP discovery. (A) Correlation between total number of discovery SNPs and number of aligned reads. The number of discovered SNPs from CTCF ChIP-seq in 10 cell lines was plotted against the number of aligned reads in each cell line. (B) Effect of increasing read depth on SNP discovery. A random sample as indicated on the X axis was taken from Progeria CTCF ChIP-seq reads and SNP discovery was performed using this subset of reads. The number of SNPs discovered in each sample as well as number of SNPs discovered in ChIP-ed regions (with at least 5X read coverage) is plotted. ChIP-ed regions were defined with the full set of reads (100% of the total reads).