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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4551-4600 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.2998 | 74.7038 | 96.7245 | 58.1245 | 15386 | 5210 | 15385 | 521 | 324 | 62.1881 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.8586 | 99.2554 | 94.5749 | 83.0098 | 9065 | 68 | 9065 | 520 | 22 | 4.2308 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.8586 | 99.2554 | 94.5749 | 83.0098 | 9065 | 68 | 9065 | 520 | 22 | 4.2308 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 26.1799 | 75.0000 | 15.8576 | 76.7407 | 93 | 31 | 98 | 520 | 4 | 0.7692 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 30.3983 | 25.0379 | 38.6792 | 58.6745 | 330 | 988 | 328 | 520 | 491 | 94.4231 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 62.9012 | 59.7110 | 66.4516 | 34.9559 | 1033 | 697 | 1030 | 520 | 432 | 83.0769 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6351 | 98.9928 | 98.2801 | 74.5158 | 30173 | 307 | 29714 | 520 | 391 | 75.1923 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6351 | 98.9928 | 98.2801 | 74.5158 | 30173 | 307 | 29714 | 520 | 391 | 75.1923 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.3294 | 95.6482 | 97.0203 | 55.0608 | 16902 | 769 | 16899 | 519 | 497 | 95.7611 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.3294 | 95.6482 | 97.0203 | 55.0608 | 16902 | 769 | 16899 | 519 | 497 | 95.7611 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 55.8033 | 65.7682 | 48.4608 | 63.2482 | 488 | 254 | 488 | 519 | 513 | 98.8439 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.3065 | 97.4471 | 87.6810 | 67.1193 | 3779 | 99 | 3694 | 519 | 13 | 2.5048 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 56.2787 | 41.6430 | 86.7771 | 58.5183 | 3371 | 4724 | 3406 | 519 | 454 | 87.4759 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | het | 2.9851 | 80.0000 | 1.5209 | 74.7722 | 8 | 2 | 8 | 518 | 2 | 0.3861 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | homalt | 12.1241 | 90.3226 | 6.4982 | 46.3178 | 28 | 3 | 36 | 518 | 433 | 83.5907 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 94.3510 | 97.7144 | 91.2114 | 71.0965 | 5002 | 117 | 5376 | 518 | 61 | 11.7761 | |
| mlin-fermikit | SNP | * | map_l250_m1_e0 | * | 45.7291 | 31.7641 | 81.6080 | 76.7628 | 2294 | 4928 | 2294 | 517 | 446 | 86.2669 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 30.2294 | 87.6521 | 0 | 0 | 224 | 517 | 58 | 11.2186 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 67.0699 | 85.4447 | 55.1993 | 68.7686 | 634 | 108 | 637 | 517 | 507 | 98.0658 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.5418 | 98.5606 | 89.0094 | 85.1964 | 4177 | 61 | 4187 | 517 | 55 | 10.6383 | |
| gduggal-bwaplat | INDEL | * | HG002compoundhet | het | 66.0619 | 55.5447 | 81.4921 | 84.3450 | 2274 | 1820 | 2272 | 516 | 182 | 35.2713 | |
| hfeng-pmm1 | INDEL | * | * | homalt | 99.6836 | 99.7787 | 99.5886 | 55.4406 | 124895 | 277 | 124903 | 516 | 501 | 97.0930 | |
| qzeng-custom | SNP | ti | map_l125_m1_e0 | * | 82.7982 | 71.8971 | 97.5960 | 82.1188 | 21091 | 8244 | 20948 | 516 | 435 | 84.3023 | |
| ckim-dragen | SNP | ti | map_l100_m0_e0 | * | 98.3169 | 98.9803 | 97.6623 | 69.9393 | 21549 | 222 | 21557 | 516 | 60 | 11.6279 | |
| ciseli-custom | INDEL | * | map_l100_m1_e0 | het | 72.9400 | 70.5593 | 75.4869 | 88.5098 | 1577 | 658 | 1589 | 516 | 305 | 59.1085 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1110 | 97.3601 | 98.8735 | 45.3846 | 35626 | 966 | 45291 | 516 | 450 | 87.2093 | |
| ciseli-custom | INDEL | D16_PLUS | HG002complexvar | * | 48.6337 | 42.4224 | 56.9758 | 58.5526 | 697 | 946 | 682 | 515 | 432 | 83.8835 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.0584 | 88.4799 | 81.8917 | 87.8767 | 2404 | 313 | 2329 | 515 | 146 | 28.3495 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1594 | 93.5769 | 94.7492 | 68.8883 | 9426 | 647 | 9275 | 514 | 466 | 90.6615 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 88.4979 | 97.7029 | 80.8780 | 52.7675 | 638 | 15 | 2174 | 514 | 354 | 68.8716 | |
| qzeng-custom | SNP | ti | map_l100_m1_e0 | het | 87.3398 | 78.8625 | 97.8592 | 80.1613 | 23613 | 6329 | 23496 | 514 | 414 | 80.5447 | |
| jlack-gatk | INDEL | I6_15 | * | homalt | 95.8674 | 99.6474 | 92.3637 | 53.5505 | 6217 | 22 | 6217 | 514 | 507 | 98.6381 | |
| hfeng-pmm2 | SNP | tv | * | * | 99.9268 | 99.9066 | 99.9471 | 21.6564 | 968784 | 906 | 968705 | 513 | 42 | 8.1871 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4259 | 96.9186 | 95.9382 | 41.0474 | 1321 | 42 | 12117 | 513 | 483 | 94.1520 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.4056 | 99.5621 | 95.3406 | 49.3281 | 10685 | 47 | 10497 | 513 | 52 | 10.1365 | |
| cchapple-custom | SNP | tv | map_l150_m2_e1 | * | 96.3274 | 97.0614 | 95.6045 | 79.4325 | 11164 | 338 | 11158 | 513 | 83 | 16.1793 | |
| cchapple-custom | SNP | tv | map_l150_m2_e1 | het | 95.2289 | 97.2237 | 93.3142 | 82.3755 | 7144 | 204 | 7160 | 513 | 83 | 16.1793 | |
| ckim-dragen | SNP | ti | map_l150_m2_e1 | * | 98.2199 | 98.8901 | 97.5587 | 78.2933 | 20493 | 230 | 20500 | 513 | 69 | 13.4503 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.3376 | 91.6367 | 95.1028 | 49.5731 | 10179 | 929 | 9943 | 512 | 284 | 55.4688 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2006 | 94.8980 | 70.9586 | 87.8472 | 1674 | 90 | 1251 | 512 | 45 | 8.7891 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7473 | 94.3151 | 97.2237 | 42.8173 | 17221 | 1038 | 17930 | 512 | 480 | 93.7500 | |
| gduggal-snapvard | INDEL | * | map_l100_m0_e0 | het | 83.1200 | 94.8090 | 73.9970 | 89.3957 | 968 | 53 | 1457 | 512 | 171 | 33.3984 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.9385 | 90.7361 | 97.3752 | 52.7808 | 18022 | 1840 | 18957 | 511 | 394 | 77.1037 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.6870 | 88.2788 | 91.1408 | 63.5606 | 5370 | 713 | 5257 | 511 | 485 | 94.9119 | |
| mlin-fermikit | SNP | ti | map_l150_m0_e0 | * | 48.0167 | 33.6471 | 83.8086 | 63.2254 | 2645 | 5216 | 2645 | 511 | 462 | 90.4110 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.4402 | 98.1388 | 92.8860 | 44.9639 | 6591 | 125 | 6659 | 510 | 472 | 92.5490 | |
| ghariani-varprowl | SNP | * | map_l250_m2_e1 | * | 95.6014 | 97.4208 | 93.8488 | 91.4722 | 7781 | 206 | 7781 | 510 | 89 | 17.4510 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 22.7901 | 26.5957 | 19.9372 | 79.3316 | 125 | 345 | 127 | 510 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 89.1203 | 97.1933 | 82.2855 | 70.9397 | 2424 | 70 | 2369 | 510 | 8 | 1.5686 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.7341 | 89.2791 | 96.4674 | 63.8560 | 13907 | 1670 | 13927 | 510 | 296 | 58.0392 | |