[Error rate calculation] quick calculation for PCR and sequencing errors
Summary Improved Q5 for PCR: 8.4*10^-4 Paired-end sequencing: 6.9*10^-5 Previous Taq for PCR: 0.162 Single read sequencing: 5.2*10^-2 ---------Explanations----------------- PCR error rate : Q5: https://www.neb.com/products/m0491-q5-high-fidelity-dna-polymerase ~280 lower than Taq https://www.neb.com/tools-and-resources/feature-articles/polymerase-fidelity-what-is-it-and-what-does-it-mean-for-your-pcr PCR_Q5 = 1.4*10^-6 PCR_Taq =2.7*10^-4 After 30 cycles of PCR amplification for 20bp barcode, The probability for one of the sites being mutated is Q5: 1.4*10^-6*20*30 = 0.00084 = 8.4*10^-4 Taq: 2.7*10^-4*20*30 = 0.162 Sequencing error rate ： The HiSeq data sets showed the lowest substitution rates of all three platforms with average rates of 0.0026 (errors per base) for R1 and 0.0040 (errors per base) for R2. For single read Error rate = 0.0026*20 = 5.2*10^-2 For paired-end seq, if we threw away reads when there is a base that is inconsis...