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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

From: Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines

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)