10× genome. Upon further review of the SNVMix2 positions predicted at 10×, but not at 40×, we examined that the majority (9 out of 13) were marginally below threshold and significant probability mass was indeed on the P(ab) state (>0.99) and would have been predicted with even a slightly less stringent threshold. Three out of the remaining four appear to be the result of DNA copy number amplifications that are skewing the allelic ratios involved. We elaborate on this point in Section 4. Table 2.Comparison of accuracy of SNVMix1, SNVMix2 and SNVMix combined with base and mapping quality thresholdingModelRunTrain AUCTPFPTNFNSensPrecF-measureSNVMix110×0.9880305192001.00000.61370.760640×0.992429310785120.96070.73250.8312SNVMix210×0.99052991623060.98030.64860.780740×0.992929010785150.95080.73050.8262SNVMix2+thresholdingmQ50_bQ20 (10×)0.988228788104180.94100.76530.8441mQ50_bQ15 (40×)0.992828771121180.94100.80170.8658
