PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9501-9550 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8084 | 91.7464 | 98.0818 | 67.8189 | 767 | 69 | 767 | 15 | 13 | 86.6667 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.0618 | 95.9514 | 98.1982 | 81.3445 | 237 | 10 | 218 | 4 | 2 | 50.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0156 | 88.8679 | 99.7963 | 48.3158 | 471 | 59 | 490 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.1875 | 100.0000 | 85.5072 | 76.2069 | 59 | 0 | 59 | 10 | 10 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0434 | 93.0771 | 95.0299 | 54.7829 | 3657 | 272 | 3652 | 191 | 179 | 93.7173 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3545 | 97.0864 | 89.8990 | 74.7771 | 933 | 28 | 890 | 100 | 90 | 90.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.3859 | 89.8140 | 99.4483 | 30.8646 | 2125 | 241 | 2163 | 12 | 11 | 91.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.5937 | 99.5017 | 88.3481 | 52.5210 | 599 | 3 | 599 | 79 | 78 | 98.7342 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.8025 | 94.1748 | 97.4874 | 88.3830 | 194 | 12 | 194 | 5 | 2 | 40.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.1564 | 94.7368 | 97.6190 | 90.9968 | 90 | 5 | 82 | 2 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.7576 | 91.8605 | 100.0000 | 77.9747 | 79 | 7 | 87 | 0 | 0 | ||
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.3396 | 100.0000 | 89.2857 | 92.7273 | 25 | 0 | 25 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7315 | 91.7481 | 97.9155 | 67.3720 | 1690 | 152 | 1691 | 36 | 30 | 83.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.1228 | 96.5257 | 97.7273 | 78.8316 | 639 | 23 | 602 | 14 | 8 | 57.1429 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.5220 | 86.1761 | 99.8768 | 41.7921 | 773 | 124 | 811 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5326 | 98.2332 | 92.9766 | 69.7368 | 278 | 5 | 278 | 21 | 21 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1978 | 98.9840 | 99.4125 | 65.8284 | 3215 | 33 | 3215 | 19 | 7 | 36.8421 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9859 | 98.8636 | 99.1085 | 68.8570 | 2001 | 23 | 2001 | 18 | 6 | 33.3333 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.5490 | 99.1830 | 99.9177 | 59.2008 | 1214 | 10 | 1214 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.3391 | 99.1425 | 99.5364 | 69.3276 | 1503 | 13 | 1503 | 7 | 2 | 28.5714 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0399 | 98.7903 | 99.2908 | 71.3498 | 980 | 12 | 980 | 7 | 2 | 28.5714 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.9045 | 99.8092 | 100.0000 | 64.4942 | 523 | 1 | 523 | 0 | 0 | ||
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.2427 | 99.0344 | 99.4519 | 67.0189 | 4718 | 46 | 4718 | 26 | 9 | 34.6154 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0037 | 98.8395 | 99.1683 | 69.7220 | 2981 | 35 | 2981 | 25 | 8 | 32.0000 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.6558 | 99.3707 | 99.9425 | 60.9526 | 1737 | 11 | 1737 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.2986 | 93.6245 | 97.0336 | 62.2347 | 3730 | 254 | 3729 | 114 | 103 | 90.3509 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5608 | 96.7376 | 96.3847 | 75.3388 | 1364 | 46 | 1333 | 50 | 40 | 80.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9517 | 89.0231 | 99.4582 | 32.2317 | 1622 | 200 | 1652 | 9 | 8 | 88.8889 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.9381 | 98.9362 | 93.1164 | 62.2579 | 744 | 8 | 744 | 55 | 55 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7823 | 92.5681 | 95.0288 | 54.7425 | 3637 | 292 | 3632 | 190 | 179 | 94.2105 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.1494 | 96.8783 | 89.6970 | 74.8348 | 931 | 30 | 888 | 102 | 92 | 90.1961 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9827 | 89.0533 | 99.4898 | 29.9773 | 2107 | 259 | 2145 | 11 | 11 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.7402 | 99.5017 | 88.6095 | 52.7933 | 599 | 3 | 599 | 77 | 76 | 98.7013 | |
| ckim-vqsr | INDEL | C6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| ckim-vqsr | INDEL | C6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| ckim-vqsr | INDEL | C6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| ckim-vqsr | INDEL | C6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6964 | 95.4417 | 95.9524 | 73.2314 | 2031 | 97 | 2015 | 85 | 77 | 90.5882 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.5214 | 97.8947 | 89.5221 | 87.3282 | 651 | 14 | 487 | 57 | 50 | 87.7193 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.2725 | 91.6923 | 99.1437 | 39.7362 | 894 | 81 | 1042 | 9 | 9 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.8852 | 99.5902 | 96.2376 | 72.0686 | 486 | 2 | 486 | 19 | 18 | 94.7368 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.0829 | 93.1978 | 97.0458 | 62.0799 | 3713 | 271 | 3712 | 113 | 105 | 92.9204 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7729 | 96.8794 | 96.6667 | 75.3175 | 1366 | 44 | 1334 | 46 | 39 | 84.7826 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.3918 | 87.9802 | 99.5128 | 30.5121 | 1603 | 219 | 1634 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1514 | 90.4452 | 98.1743 | 66.8941 | 1666 | 176 | 1667 | 31 | 27 | 87.0968 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.0443 | 95.9215 | 98.1938 | 78.8174 | 635 | 27 | 598 | 11 | 7 | 63.6364 | |