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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4151-4200 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 90.6674 | 96.3091 | 85.6501 | 61.6361 | 3627 | 139 | 3623 | 607 | 603 | 99.3410 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 90.6674 | 96.3091 | 85.6501 | 61.6361 | 3627 | 139 | 3623 | 607 | 603 | 99.3410 | |
| ghariani-varprowl | SNP | * | map_l150_m0_e0 | * | 96.3674 | 97.6729 | 95.0963 | 84.3053 | 11752 | 280 | 11752 | 606 | 137 | 22.6073 | |
| egarrison-hhga | SNP | ti | * | het | 99.8877 | 99.8228 | 99.9527 | 17.2025 | 1279619 | 2272 | 1279622 | 606 | 80 | 13.2013 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | homalt | 87.1292 | 84.9759 | 89.3945 | 70.0273 | 5113 | 904 | 5108 | 606 | 472 | 77.8878 | |
| ciseli-custom | INDEL | I1_5 | map_siren | het | 73.5105 | 78.9411 | 68.7790 | 81.4258 | 1327 | 354 | 1335 | 606 | 517 | 85.3135 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2808 | 99.8350 | 96.7742 | 42.6049 | 18153 | 30 | 18150 | 605 | 8 | 1.3223 | |
| gduggal-bwavard | SNP | tv | map_l250_m1_e0 | * | 88.5182 | 97.6199 | 80.9689 | 91.3881 | 2584 | 63 | 2574 | 605 | 16 | 2.6446 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | het | 92.7126 | 88.1229 | 97.8066 | 81.8391 | 26985 | 3637 | 26978 | 605 | 56 | 9.2562 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 59.1529 | 51.0315 | 70.3486 | 60.3619 | 940 | 902 | 1433 | 604 | 512 | 84.7682 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4108 | 95.2812 | 97.5675 | 40.2387 | 23382 | 1158 | 24186 | 603 | 555 | 92.0398 | |
| ciseli-custom | INDEL | I6_15 | HG002compoundhet | het | 17.3297 | 18.2692 | 16.4820 | 51.6410 | 38 | 170 | 119 | 603 | 564 | 93.5323 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 93.6725 | 99.5667 | 88.4372 | 45.0706 | 4596 | 20 | 4612 | 603 | 12 | 1.9901 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | het | 84.7648 | 91.3462 | 79.0682 | 44.3175 | 190 | 18 | 2274 | 602 | 437 | 72.5914 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| gduggal-bwavard | SNP | * | map_l250_m0_e0 | * | 85.5739 | 96.0656 | 77.1483 | 94.8205 | 2051 | 84 | 2029 | 601 | 15 | 2.4958 | |
| jpowers-varprowl | SNP | ti | map_l100_m1_e0 | * | 98.2270 | 97.7259 | 98.7332 | 68.5176 | 46841 | 1090 | 46843 | 601 | 190 | 31.6140 | |
| jpowers-varprowl | SNP | ti | map_l100_m2_e1 | het | 97.5492 | 97.0640 | 98.0394 | 72.8908 | 30051 | 909 | 30053 | 601 | 165 | 27.4542 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 48.7545 | 54.7591 | 43.9366 | 94.6836 | 466 | 385 | 471 | 601 | 36 | 5.9900 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 8.8851 | 13.8889 | 6.5319 | 87.2673 | 40 | 248 | 42 | 601 | 6 | 0.9983 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 78.4884 | 95.1433 | 66.7958 | 80.7253 | 1195 | 61 | 1207 | 600 | 372 | 62.0000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.4046 | 90.2930 | 96.7382 | 47.0617 | 17934 | 1928 | 17795 | 600 | 351 | 58.5000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.3331 | 99.7813 | 95.0021 | 46.2479 | 11408 | 25 | 11405 | 600 | 4 | 0.6667 | |
| ndellapenna-hhga | INDEL | * | HG002complexvar | homalt | 98.2704 | 98.7420 | 97.8033 | 53.5832 | 26687 | 340 | 26669 | 599 | 404 | 67.4457 | |
| gduggal-bwavard | SNP | tv | map_l250_m1_e0 | het | 84.6644 | 98.0974 | 74.4672 | 92.2745 | 1753 | 34 | 1747 | 599 | 12 | 2.0033 | |
| ckim-gatk | SNP | ti | map_l100_m2_e1 | * | 90.0482 | 82.8877 | 98.5628 | 78.3843 | 41017 | 8468 | 41010 | 598 | 70 | 11.7057 | |
| cchapple-custom | SNP | ti | map_l150_m1_e0 | * | 96.7874 | 96.6213 | 96.9540 | 76.8102 | 19046 | 666 | 19034 | 598 | 159 | 26.5886 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 38.9035 | 36.0279 | 42.2780 | 67.7158 | 361 | 641 | 438 | 598 | 312 | 52.1739 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 55.7305 | 44.0570 | 75.8202 | 34.2652 | 1731 | 2198 | 1872 | 597 | 591 | 98.9950 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 54.8241 | 40.1571 | 86.3699 | 66.0570 | 3731 | 5560 | 3783 | 597 | 508 | 85.0921 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 54.8241 | 40.1571 | 86.3699 | 66.0570 | 3731 | 5560 | 3783 | 597 | 508 | 85.0921 | |
| cchapple-custom | SNP | ti | map_l150_m1_e0 | het | 95.9987 | 96.7583 | 95.2510 | 80.3175 | 11969 | 401 | 11974 | 597 | 158 | 26.4657 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 77.6919 | 72.9319 | 83.1165 | 45.6084 | 2689 | 998 | 2939 | 597 | 575 | 96.3149 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8464 | 98.6772 | 97.0296 | 69.0281 | 19320 | 259 | 19501 | 597 | 25 | 4.1876 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8464 | 98.6772 | 97.0296 | 69.0281 | 19320 | 259 | 19501 | 597 | 25 | 4.1876 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 60.0456 | 65.5567 | 55.3892 | 58.1977 | 630 | 331 | 740 | 596 | 423 | 70.9732 | |
| gduggal-snapvard | INDEL | D1_5 | map_siren | * | 89.9255 | 93.9643 | 86.2197 | 83.0558 | 3316 | 213 | 3729 | 596 | 269 | 45.1342 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | * | 92.1390 | 91.0641 | 93.2396 | 35.4470 | 8224 | 807 | 8220 | 596 | 552 | 92.6174 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.7432 | 96.5626 | 94.9376 | 45.0963 | 11040 | 393 | 11177 | 596 | 251 | 42.1141 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.0746 | 98.4739 | 97.6786 | 54.4653 | 24972 | 387 | 25036 | 595 | 449 | 75.4622 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 52.7646 | 70.1389 | 42.2890 | 66.9445 | 202 | 86 | 436 | 595 | 310 | 52.1008 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 90.3941 | 93.8999 | 87.1407 | 79.9532 | 4033 | 262 | 4032 | 595 | 11 | 1.8487 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 85.6204 | 89.4628 | 82.0945 | 59.1015 | 866 | 102 | 2728 | 595 | 253 | 42.5210 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1771 | 97.9914 | 98.3635 | 52.4340 | 35857 | 735 | 35764 | 595 | 553 | 92.9412 | |
| jpowers-varprowl | SNP | ti | map_l100_m2_e0 | het | 97.5401 | 97.0479 | 98.0373 | 72.8725 | 29718 | 904 | 29720 | 595 | 164 | 27.5630 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.2904 | 99.2602 | 97.3394 | 75.4562 | 21737 | 162 | 21732 | 594 | 582 | 97.9798 | |
| gduggal-bwavard | SNP | * | map_l250_m0_e0 | het | 81.4711 | 96.1487 | 70.6811 | 95.2079 | 1448 | 58 | 1432 | 594 | 10 | 1.6835 | |