Table 4

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 Q30 # 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
BCV 79,037x 20413 2133 152 19% 0%
Fox1 80,546x 14472 1354 70 21% 0%
Fox2 96,198x 20417 1596 88 26% 0%

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

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