TABLE 2.
Estimated sequencing error rates based on replicates and controlsa
| Prior amplification | Control expt assembly | Reference assembly | No. of substitution errors | No. of correct bases | Error rate (per base) | Mean error rate (per base) |
|---|---|---|---|---|---|---|
| No amplification | Jijoye | Jiyoye assembly* | 1 | 134,118 | 7.46E−06 | 1.13E−05 |
| Daudi | Daudi assembly* | 0 | 132,780 | 0.00E+00 | 1.13E−05 | |
| Raji_Rep1 | Raji assembly* | 0 | 130,560 | 0.00E+00 | 1.13E−05 | |
| Raji_Rep2 | Raji assembly* | 5 | 132,736 | 3.77E−05 | 1.13E−05 | |
| GenomiPhi-WGA | Raji_wga | Raji assembly* | 2 | 132,836 | 1.51E−05 | 2.13E−05 |
| eBLtumor-01_EBV_type1_wga | eBLtumor-01_EBV_type1# | 1 | 140,069 | 7.14E−06 | 2.13E−05 | |
| eBLtumor-02_EBV_type2_wga | eBLtumor-02_EBV_type2# | 4 | 142,932 | 2.80E−05 | 2.13E−05 | |
| eBLtumor-03_EBV_type2_wga | eBLtumor-03_EBV_type2# | 1 | 142,154 | 7.03E−06 | 2.13E−05 | |
| eBLtumor-04_EBV_type1_wga | eBLtumor-04_EBV_type1# | 5 | 141,643 | 3.53E−05 | 2.13E−05 | |
| eBLtumor-05_EBV_type1_wga | eBLtumor-05_EBV_type1# | 5 | 141,643 | 3.53E−05 | 2.13E−05 | |
| mlrPCR-sWGA | Raji_Rep1_mlrPCR-sWGA | Raji assembly* | 6 | 98,507 | 6.09E−05 | 1.09E−04 |
| Raji_Rep2_mlrPCR-sWGA | Raji assembly* | 11 | 130,538 | 8.43E−05 | 1.09E−04 | |
| Jijoye_Rep1_mlrPCR-sWGA | Jiyoye assembly* | 13 | 132,045 | 9.84E−05 | 1.09E−04 | |
| Daudi_mlrPCR-sWGA | Daudi assembly* | 25 | 130,160 | 1.92E−04 | 1.09E−04 |
a
*, Reference assemblies are from Palser et al. (34) (Jijoye, LN827800; Daudi, LN827545; and Raji, KF717093). #, The indicated isolates were sequenced without any amplification. Preprocess denotes whether the sample DNA was amplified prior to sequencing library preparation. The numbers of substitutions were determined by pairwise whole-genome alignments of control and reference assemblies. Error rates refer to the average mismatches to reference assemblies after normalizing to total covered genomic regions. GenomiPhi-WGA, whole-genome amplification using EBV-specific protected hexamers; mlrPCR-sWGA, preamplification with PCR primer pools followed by sWGA.