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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78501-78550 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | * | HG002compoundhet | * | 99.3639 | 98.9737 | 99.7572 | 37.9767 | 25557 | 265 | 25473 | 62 | 19 | 30.6452 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | het | 99.2921 | 98.9773 | 99.6090 | 42.0270 | 14033 | 145 | 14011 | 55 | 13 | 23.6364 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | hetalt | 99.7674 | 99.5360 | 100.0000 | 21.7668 | 858 | 4 | 859 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | * | HG002compoundhet | homalt | 99.4265 | 98.9241 | 99.9340 | 32.8863 | 10666 | 116 | 10603 | 7 | 6 | 85.7143 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | * | 99.3879 | 98.9873 | 99.7918 | 33.3089 | 17301 | 177 | 17255 | 36 | 13 | 36.1111 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | het | 99.3400 | 99.0005 | 99.6817 | 37.0509 | 9410 | 95 | 9396 | 30 | 8 | 26.6667 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | hetalt | 99.7403 | 99.4819 | 100.0000 | 21.4966 | 576 | 3 | 577 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | homalt | 99.4222 | 98.9316 | 99.9177 | 28.6749 | 7315 | 79 | 7282 | 6 | 5 | 83.3333 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | * | 98.0840 | 96.8760 | 99.3225 | 65.2361 | 11970 | 386 | 11875 | 81 | 56 | 69.1358 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | het | 95.9122 | 96.4706 | 95.3602 | 73.5551 | 820 | 30 | 781 | 38 | 14 | 36.8421 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | hetalt | 98.4111 | 97.0028 | 99.8609 | 64.1248 | 10842 | 335 | 10768 | 15 | 15 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | homalt | 92.8474 | 93.6170 | 92.0904 | 71.4055 | 308 | 21 | 326 | 28 | 27 | 96.4286 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | * | 99.3414 | 98.9802 | 99.7052 | 44.7928 | 8832 | 91 | 8795 | 26 | 6 | 23.0769 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | het | 99.1949 | 98.9300 | 99.4612 | 50.0484 | 4623 | 50 | 4615 | 25 | 5 | 20.0000 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | hetalt | 99.7674 | 99.5360 | 100.0000 | 21.7668 | 858 | 4 | 859 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | homalt | 99.4361 | 98.9079 | 99.9699 | 40.5831 | 3351 | 37 | 3321 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002compoundhet | * | 88.6244 | 82.1745 | 96.1730 | 41.5559 | 1761 | 382 | 1734 | 69 | 67 | 97.1014 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002compoundhet | het | 69.4745 | 61.7021 | 79.4872 | 79.6875 | 29 | 18 | 31 | 8 | 7 | 87.5000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 90.2840 | 82.6087 | 99.5316 | 37.2520 | 1729 | 364 | 1700 | 8 | 8 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002compoundhet | homalt | 10.1695 | 100.0000 | 5.3571 | 67.2515 | 3 | 0 | 3 | 53 | 52 | 98.1132 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | * | 67.1085 | 66.3284 | 67.9072 | 58.7807 | 19872 | 10088 | 19761 | 9339 | 9228 | 98.8114 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | het | 43.9232 | 77.6258 | 30.6263 | 58.8856 | 3178 | 916 | 2983 | 6757 | 6682 | 98.8900 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | hetalt | 77.7377 | 63.7887 | 99.4948 | 53.3255 | 16062 | 9118 | 16150 | 82 | 81 | 98.7805 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | homalt | 32.9688 | 92.1283 | 20.0767 | 74.2148 | 632 | 54 | 628 | 2500 | 2465 | 98.6000 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | * | 98.1691 | 96.6358 | 99.7519 | 35.8566 | 16890 | 588 | 16888 | 42 | 17 | 40.4762 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | het | 98.1344 | 96.5702 | 99.7500 | 39.9164 | 9179 | 326 | 9177 | 23 | 14 | 60.8696 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | hetalt | 95.8808 | 94.4732 | 97.3310 | 25.3652 | 547 | 32 | 547 | 15 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | homalt | 98.3931 | 96.8894 | 99.9442 | 30.6032 | 7164 | 230 | 7164 | 4 | 3 | 75.0000 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | * | 94.5808 | 93.8213 | 95.3528 | 36.4670 | 8473 | 558 | 8474 | 413 | 394 | 95.3995 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | het | 89.0353 | 96.6121 | 82.5605 | 68.4177 | 827 | 29 | 819 | 173 | 168 | 97.1098 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 96.1166 | 93.5100 | 98.8728 | 25.0680 | 7622 | 529 | 7631 | 87 | 83 | 95.4023 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | homalt | 23.8806 | 100.0000 | 13.5593 | 67.6417 | 24 | 0 | 24 | 153 | 143 | 93.4641 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | * | 93.7345 | 93.5147 | 93.9554 | 62.6967 | 28017 | 1943 | 27901 | 1795 | 1783 | 99.3315 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | het | 92.6752 | 98.3879 | 87.5896 | 79.6233 | 4028 | 66 | 3790 | 537 | 528 | 98.3240 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | hetalt | 96.0304 | 92.5536 | 99.7785 | 50.2300 | 23305 | 1875 | 23427 | 52 | 52 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | homalt | 53.1056 | 99.7085 | 36.1905 | 83.1205 | 684 | 2 | 684 | 1206 | 1203 | 99.7512 | |
| asubramanian-gatk | INDEL | I6_15 | HG002compoundhet | * | 93.0480 | 91.1691 | 95.0059 | 37.8731 | 8001 | 775 | 8009 | 421 | 405 | 96.1995 | |
| asubramanian-gatk | INDEL | I6_15 | HG002compoundhet | het | 83.5162 | 93.2692 | 75.6098 | 84.8597 | 194 | 14 | 155 | 50 | 46 | 92.0000 | |
| asubramanian-gatk | INDEL | I6_15 | HG002compoundhet | hetalt | 94.9935 | 91.0859 | 99.2515 | 30.1736 | 7776 | 761 | 7823 | 59 | 55 | 93.2203 | |
| asubramanian-gatk | INDEL | I6_15 | HG002compoundhet | homalt | 16.5775 | 100.0000 | 9.0379 | 62.9989 | 31 | 0 | 31 | 312 | 304 | 97.4359 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | * | 97.7516 | 96.6501 | 98.8785 | 41.8929 | 24957 | 865 | 24950 | 283 | 28 | 9.8940 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | het | 97.7049 | 96.5369 | 98.9015 | 46.6042 | 13687 | 491 | 13685 | 152 | 23 | 15.1316 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | hetalt | 95.0437 | 94.5476 | 95.5451 | 26.8439 | 815 | 47 | 815 | 38 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | homalt | 98.0307 | 96.9672 | 99.1179 | 35.4971 | 10455 | 327 | 10450 | 93 | 5 | 5.3763 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 92.8089 | 90.2940 | 95.4680 | 54.0308 | 1935 | 208 | 1938 | 92 | 88 | 95.6522 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | het | 80.8415 | 91.4894 | 72.4138 | 94.0574 | 43 | 4 | 21 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 94.3857 | 90.2532 | 98.9147 | 46.6501 | 1889 | 204 | 1914 | 21 | 21 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.6957 | 100.0000 | 4.5455 | 78.0731 | 3 | 0 | 3 | 63 | 59 | 93.6508 | |
| asubramanian-gatk | INDEL | I1_5 | HG002compoundhet | * | 95.2373 | 93.5902 | 96.9436 | 67.0365 | 11564 | 792 | 11577 | 365 | 350 | 95.8904 | |
| asubramanian-gatk | INDEL | I1_5 | HG002compoundhet | het | 93.5851 | 96.0000 | 91.2888 | 86.8239 | 816 | 34 | 765 | 73 | 70 | 95.8904 | |