Table 3.
Comparison of variant calls for M3 (MiSeq) and M4 (NextSeq) sequencing of the N12878 reference sample with the Genome in a Bottle high confidence variant call set
| Sequencer | Variant type | TP | FP | FN | TN | Sensitivity (%)a | Precision (%)b | MCC (%)c |
|---|---|---|---|---|---|---|---|---|
| MiSeq | All | 249 | 0 | 1 | 522509 | 99.6 | 100 | 99.8 |
| MiSeq | SNVs | 245 | 0 | 0 | 522518 | 100 | 100 | 100 |
| MiSeq | Indels | 4 | 0 | 1 | 522754 | 0.80 | 100 | 89.4 |
| NextSeq | All | 249 | 1 | 1 | 522508 | 99.6 | 99.6 | 99.6 |
| NextSeq | SNVs | 245 | 1 | 0 | 522517 | 100 | 99.6 | 99.8 |
| NextSeq | Indels | 4 | 0 | 1 | 522754 | 0.80 | 100 | 89.4 |
Analysis was done over a 522,763 bp region corresponding to protein-coding region ±8 bps that overlaps with the GIAB high confidence regions
TP true positive, FP false positive, FN false negative, MCC Matthews correlation coefficient
aSensitivity = TP / (TP + FN)
bPrecision = TP / (TP + FP)
cMCC = (TP × TN) − (FP × FN) / √[(TP + FP)(TP + FN)(TN + FP)(TN + FN)]