Table 1 Comparing sensitivity and specificity to coverage achieved for three sets of multiplexes
All allele frequencies | ≤5% MAF | 2% MAF(4 alleles in pool) | 0.5% MAF(1 allele in pool) | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Size Multiplex | Coverage | Percent of Bases, average (SD) | Homozygous wild type sites | Heterozygous sites | Homozygous variant sites | Sensitivity average (SD) | Specificity, average (SD) | Homozygous wild-type sites | Heterozygous sites | Homozygous variant sites | Sensitivity (avg) | Specificity (avg) | Heterozygous sites | Sensitivity (avg) | Specificity (avg) | Heterozygous sites | Sensitivity (avg) | Specificity (avg) |
22-24 | ≥3 | 84.4(1.29) | 229483 | 39100 | 24855 | 95.02(1.42) | 99.82(0.14) | 172205 | 2057 | 20 | 92.49 | 99.98 | 656 | 91.6 | 99.98 | 127 | 88.3 | 99.99 |
≥5 | 84.6(1.75) | 221031 | 37332 | 23810 | 96.75(1.23) | 99.82(0.14) | 166050 | 1961 | 19 | 95.30 | 99.98 | 624 | 94.9 | 99.99 | 119 | 90.2 | 99.99 | |
≥10 | 75.0(2.65) | 201268 | 33626 | 21451 | 98.22(0.98) | 99.86(0.13) | 151395 | 1768 | 17 | 97.42 | 99.98 | 563 | 96.6 | 99.99 | 111 | 93.8 | 100 | |
≥15 | 67.1(3.57) | 182332 | 30279 | 19510 | 98.60(0.93) | 99.88(0.12) | 137327 | 1579 | 17 | 98.50 | 99.98 | 507 | 98.0 | 99.99 | 100 | 96.0 | 100 | |
≥20 | 59.8(4.51) | 163986 | 27202 | 17643 | 98.94(0.83) | 99.89(0.12) | 123572 | 1418 | 14 | 98.81 | 99.98 | 460 | 98.7 | 100 | 90 | 95.6 | 100 | |
48 | ≥3 | 89.0(2.30) | 239300 | 39218 | 26310 | 95.80(1.42) | 99.90(0.08) | 187077 | 2109 | 25 | 92.97 | 99.97 | 651 | 92.9 | 99.99 | 131 | 94.7 | 100 |
≥5 | 84.1(3.14) | 230685 | 37434 | 25232 | 96.43(0.95) | 99.91(0.08) | 179900 | 1997 | 25 | 95.95 | 99.97 | 619 | 95.8 | 99.99 | 125 | 96.8 | 100 | |
≥10 | 74.8(4.54) | 209960 | 33448 | 22739 | 98.96(0.51) | 99.94(0.07) | 163128 | 1805 | 22 | 98.30 | 99.97 | 566 | 98.4 | 99.99 | 111 | 100 | 100 | |
≥15 | 67.1(5.79) | 190652 | 30010 | 20491 | 99.33(0.42) | 99.95(0.07) | 147843 | 1630 | 19 | 98.85 | 99.97 | 517 | 99.0 | 99.99 | 100 | 100 | 100 | |
≥20 | 60.3(6.98) | 172373 | 26937 | 18505 | 99.60(0.37) | 99.96(0.06) | 133259 | 1449 | 18 | 99.05 | 99.97 | 467 | 99.6 | 100 | 88 | 100 | 100 | |
30-32 | ≥3 | 89.2(2.55) | 245952 | 40732 | 26487 | 96.52(1.08) | 99.97(0.03) | 184498 | 1903 | 16 | 93.54 | 99.97 | 664 | 95.6 | 99.98 | 102 | 97.1 | 99.99 |
≥5 | 84.4(3.49) | 235796 | 38696 | 25251 | 98.23(0.69) | 99.97(0.03) | 177279 | 1809 | 16 | 96.33 | 99.97 | 644 | 97.1 | 99.99 | 102 | 97.1 | 100 | |
≥10 | 74.8(5.35) | 212716 | 34440 | 22505 | 99.43(0.40) | 99.97(0.03) | 160352 | 1600 | 14 | 98.88 | 99.97 | 567 | 99.1 | 99.99 | 99 | 96.8 | 100 | |
≥15 | 66.8(7.25) | 192642 | 30957 | 20272 | 99.80(0.19) | 99.98(0.03) | 145504 | 1403 | 12 | 99.58 | 99.98 | 497 | 99.4 | 100 | 82 | 97.6 | 100 | |
≥20 | 59.5(9.08) | 173212 | 27775 | 18237 | 99.90(0.15) | 99.98(0.03) | 130959 | 1260 | 10 | 99.76 | 99.98 | 448 | 99.6 | 100 | 72 | 98.8 | 100 | |