Relationship of read (RMD) (A), folded variant frequency (FVF) (B), and SNP mapping quality score (MQS) (C), with the rate of true - positive SNPs (blue dots) and the rate of genotype SNPS. Graphs are based on Infinium genotyping data of 6,000 selected SNPs and corresponding data of RMD, FVF and MQS in SNP discovery. The rate of true-positive SNPs was the number of true SNPs at an RMD, an FVF or an MQS value divided by the total number of genotyped SNPs (including both true- and false-positive SNPs) at the specific RMD, FVF or MQS. Similarly, the rate of genotyped SNPs was the number of genotyped SNPs at a specific RMD, FVF or MQS divided by the total number of SNPs (including both failed and genotyped SNPs) at the specific RMD, FVF or MQS.
You et al. BMC Genomics 2012 13:354 doi:10.1186/1471-2164-13-354