Fig. 3
From: High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing
SNPs-seq data analysis and BAB score distribution. a Size distribution of SNPs-seq libraries. Test samples show 150–500 bp length while input samples show ~160 bp. b Mapping of allele-specific read counts. Percentage of mapped read count is ~60% for test samples and ~95% for input controls. c Correlation between technical replicates. Mapped read counts were first transformed to log2 values, and then plotted along x (replicate 1) and y (replicate 2) axis. d Association of read count with GC content. Low GC content is significantly associated with low read count. e Association of read counts with delta G value. More thermostability of oligo duplex (lower delta G) contributes to higher read counts in SNPs-seq library. f Association of read counts with nucleotides at 5′ end. The nucleotides A, T, AA, AT, TA, or TT at 5′ end have the lowest read counts among all tested oligos. The upper, middle, and lower bounds of boxes represent the 75th, 50th, and 25th percentile of the values, respectively. The whiskers represent 95th to 5th percentile. g Overall distribution of BAB scores among the 374 tested candidate SNPs. The red line represents BAB scores in ETH group while the blue dots represent the corresponding BAB scores from the DHT group
