Table 1 Monte Carlo simulation-based comparison of the observed and expected number of variants uniquely detected by each experimental approach and in the intersection of all setups. The difference between the observed and expected distributions was significant for both SNPs and indels (chi-square test, p < 2.2 × 10− 16). Furthermore, the observed versus expected ratios of unique variants under each setup and in the intersection of all setups were all significantly higher than 1, as indicated by the 95% confidence intervals. CI: Confidence interval, CG: Complete Genomics; MOL: Illumina HiSeq; HSX: Illumina HiSeq X
Setup | SNPs | indels | ||||
|---|---|---|---|---|---|---|
Observed | Expected | Ratio (95% CI) | Observed | Expected | Ratio (95% CI) | |
CG unique | 83,820 | 449 | 186.51 (170.71 to 205.96) | 47,640 | 6602 | 7.22 (7.05 to 7.38) |
MOL + Isaac unique | 46,188 | 556 | 83.05 (76.22 to 90.75) | 31,978 | 5994 | 5.33 (5.21 to 5.47) |
HSX + Isaac unique | 84,587 | 881 | 96.05 (90.08 to 102.78) | 55,376 | 17,455 | 3.17 (3.13 to 3.22) |
MOL + GATK unique | 25,309 | 530 | 47.75 (43.94 to 52.18) | 37,960 | 24,442 | 1.55 (1.54 to 1.57) |
HSX + GATK unique | 40,320 | 633 | 63.67 (59.03 to 68.93) | 148,008 | 51,200 | 2.89 (2.87 to 2.91) |
Intersection all | 2,942,659 | 2,087,460 | 1.41 (1.409 to 1.41) | 214,730 | 42,853 | 5.01 (4.97 to 5.05) |