Table 7. Reproducibility of platform-wide variant detection among 47 samples.

n = 1240 unique variants n = 1,390,040 data points
Variant Type	Unique Variants	Concordant Data Points	Reproducibility (95% CI)
Substitutions	898	1,002,981 of 1,006,658	99.63% (99.62%, 99.65%)
Substitution in a non-repetitive region or a repetitive region of ≤7 base pairs	882	985,150 of 988,722	99.64% (99.63%, 99.65%)
Substitution in a repetitive region of >7 base pairs	16	17,831 of 17,936	99.41% (99.29%, 99.52%)
Indels	228	254,509 of 255,588	99.58% (99.55%, 99.60%)
Indel in non-repetitive region or a repetitive region of ≤3 base pairs	52	58,054 of 58,292	99.59% (99.54%, 99.64%)
Indel in a repetitive region of 4 to 6 base pairs	118	131,816 of 132,278	99.65% (99.62%, 99.68%)
Indel in a repetitive region of ≥7 base pairs	58	64,639 of 65,018	99.42% (99.36%, 99.47%)
Rearrangements	60	66,723 of 67,260	99.20% (99.13%, 99.27%)
Copy Number Alterations	54	60,115 of 60,534	99.31% (99.24%, 99.37%)
Copy Number Amplification (4–5 copies)	1	1,121 of 1,121	100.00% (99.67%, 100.00%)
Copy Number Amplification (>6 copies)	48	53,402 of 53,808	99.25% (99.17%, 99.32%)
Copy Number Loss	5	5,592 of 5,605	99.77% (99.60%, 99.88%)
Total	1240	1,384,328 of 1,390,040	99.59% (99.58%, 99.60%)

CI = confidence interval