Table 3 Sequencing and variant calling errors of next-generation sequencing based on the data set of Sanger sequences of 13 AL8/78 BAC clones
Error type | Platform | Overall error rate | INDEL error rate | Substitution error rate | Insertion (%) | Deletion (%) | Substitution (%) |
|---|---|---|---|---|---|---|---|
Sequencing error compared with Sanger sequences | |||||||
Single read error | Roche 454 GS-FLX Titanium | 7.4 × 10-3 | 6.2 × 10-3 | 1.2 × 10-3 | 42.41 | 41.93 | 15.66 |
Consensus error | Roche 454 GS-FLX Titanium | 1.3 × 10-3 | 1.0 × 10-3 | 3.0 × 10-4 | 25.20 | 55.56 | 19.24 |
|  | Illumina Solexa | 4.4 × 10-4 | 9.0 × 10-5 | 3.5 × 10-4 | 3.46 | 17.78 | 78.77 |
|  | AB SOLiD v2.0 | 4.3 × 10-4 | 2.5 × 10-4 | 1.8 × 10-4 | 10.69 | 47.58 | 41.73 |
Variant calling errors using Roche 454 sequence as reference | |||||||
Consensus error | Roche 454 GS-FLX Titanium | 3.79 × 10-3 | 1.12 × 10-3 | 2.67 × 10-3 | 11.82 | 17.66 | 70.52 |
|  | Illumina Solexa | 1.87 × 10-3 | 4.1 × 10-4 | 1.46 × 10-3 | 8.41 | 13.7 | 77.87 |
|  | AB SOLiD v2.0 | 5.9 × 10-4 | 2.7 × 10-4 | 3.2 × 10-4 | 21.71 | 24.67 | 53.62 |