|Summary of coverage, total number of candidate variants (all polymorphisms) and number variants called by the variant detection model in Q30 ORP for the 3 natural viral samples|
|Natural sample||Mean ORP coverage||# candidate variant calls at Q≥30||# variants called at error rate 5×10-5||# variants called at error rate 5×10-4||FDR for error rate 5×10-5||FDR for error rate 5×10-4|
The number of candidate variants served as the Bonferroni correction factors in the variant detection model. The number of false discoveries in each sample at error rate 5×10-5 is estimated by taking 2% (coverage adjusted false positive rate derived from control plasmids, Additional file 1: Table S2, ) of the number of candidate variants. The false discovery rate (FDR) is the proportion of false discoveries among variants discovered, e.g. for BCV, it’s the ratio between 2% of 20413 and 2133, i.e.19%. FDR at 5×10-4 is 0% for all samples since the estimated false positive rate at this error rate is 0% (Additional file 1: Table S2).
Chen-Harris et al.
Chen-Harris et al. BMC Genomics 2013 14:96 doi:10.1186/1471-2164-14-96