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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
44601-44650 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 50.1574 | 67.0715 | 40.0560 | 49.5050 | 497 | 244 | 1573 | 2354 | 1678 | 71.2829 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 60.4452 | 67.0715 | 55.0104 | 41.9298 | 2982 | 1464 | 4754 | 3888 | 3114 | 80.0926 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 76.0331 | 67.0590 | 87.7802 | 43.4475 | 11850 | 5821 | 12686 | 1766 | 1744 | 98.7542 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 76.0331 | 67.0590 | 87.7802 | 43.4475 | 11850 | 5821 | 12686 | 1766 | 1744 | 98.7542 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m0_e0 | homalt | 79.8653 | 67.0588 | 98.7179 | 91.2752 | 57 | 28 | 77 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 79.7299 | 67.0588 | 98.3051 | 62.1795 | 57 | 28 | 58 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m0_e0 | * | 78.8389 | 67.0350 | 95.6882 | 90.8414 | 364 | 179 | 577 | 26 | 10 | 38.4615 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 68.7702 | 67.0305 | 70.6027 | 63.8943 | 3808 | 1873 | 5471 | 2278 | 1700 | 74.6269 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e1 | * | 80.0171 | 67.0251 | 99.2569 | 92.4026 | 935 | 460 | 935 | 7 | 2 | 28.5714 | |
| ciseli-custom | SNP | ti | map_l250_m2_e1 | * | 70.8062 | 67.0213 | 75.0441 | 92.1332 | 3402 | 1674 | 3401 | 1131 | 218 | 19.2750 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 76.4134 | 67.0154 | 88.8773 | 44.0708 | 9224 | 4540 | 2557 | 320 | 196 | 61.2500 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 73.7796 | 66.9983 | 82.0883 | 30.1926 | 404 | 199 | 1934 | 422 | 418 | 99.0521 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.7416 | 66.9975 | 98.4728 | 66.8746 | 10329 | 5088 | 9672 | 150 | 125 | 83.3333 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 79.0601 | 66.9823 | 96.4515 | 82.5174 | 3749 | 1848 | 3751 | 138 | 63 | 45.6522 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 77.4499 | 66.9661 | 91.8256 | 57.9851 | 671 | 331 | 674 | 60 | 42 | 70.0000 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | homalt | 79.9782 | 66.9643 | 99.2706 | 72.9194 | 5100 | 2516 | 5036 | 37 | 37 | 100.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 77.5741 | 66.9623 | 92.1827 | 77.2517 | 906 | 447 | 908 | 77 | 24 | 31.1688 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 75.6857 | 66.9578 | 87.0301 | 80.4555 | 460 | 227 | 463 | 69 | 64 | 92.7536 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 66.9535 | 0.0000 | 0.0000 | 6224 | 3072 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 66.9521 | 0.0000 | 0.0000 | 391 | 193 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l125_m1_e0 | het | 79.9258 | 66.9495 | 99.1416 | 88.1040 | 12229 | 6037 | 12243 | 106 | 30 | 28.3019 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e0 | het | 79.9285 | 66.9418 | 99.1669 | 89.4354 | 19626 | 9692 | 19640 | 165 | 44 | 26.6667 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 69.9850 | 66.9291 | 73.3333 | 68.5864 | 85 | 42 | 88 | 32 | 20 | 62.5000 | |
| mlin-fermikit | INDEL | * | segdup | hetalt | 80.1843 | 66.9231 | 100.0000 | 93.8999 | 87 | 43 | 89 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 74.7342 | 66.9196 | 84.6154 | 62.9705 | 882 | 436 | 924 | 168 | 144 | 85.7143 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 70.8955 | 66.9014 | 75.3968 | 42.7273 | 95 | 47 | 95 | 31 | 29 | 93.5484 | |
| ckim-gatk | SNP | tv | map_l150_m1_e0 | * | 79.1583 | 66.8988 | 96.9190 | 88.8068 | 7300 | 3612 | 7298 | 232 | 8 | 3.4483 | |
| jmaeng-gatk | SNP | tv | map_l125_m0_e0 | het | 78.5795 | 66.8939 | 95.2119 | 92.0071 | 2944 | 1457 | 2943 | 148 | 6 | 4.0541 | |
| ciseli-custom | SNP | ti | map_l250_m2_e0 | * | 70.7049 | 66.8930 | 74.9776 | 92.1064 | 3350 | 1658 | 3350 | 1118 | 211 | 18.8730 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m1_e0 | homalt | 80.0809 | 66.8919 | 99.7481 | 73.7260 | 396 | 196 | 396 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 79.6945 | 66.8919 | 98.5577 | 39.0625 | 99 | 49 | 615 | 9 | 9 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 80.1527 | 66.8790 | 100.0000 | 72.1485 | 105 | 52 | 105 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 66.8748 | 0.0000 | 0.0000 | 4605 | 2281 | 0 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 72.8176 | 66.8723 | 79.9231 | 50.7780 | 1843 | 913 | 1871 | 470 | 429 | 91.2766 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e1 | het | 79.5911 | 66.8582 | 98.3146 | 91.5439 | 349 | 173 | 350 | 6 | 2 | 33.3333 | |
| ghariani-varprowl | INDEL | I6_15 | segdup | * | 72.0984 | 66.8571 | 78.2313 | 93.2039 | 117 | 58 | 115 | 32 | 32 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 79.3333 | 66.8539 | 97.5410 | 81.8452 | 119 | 59 | 119 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.6619 | 66.8539 | 87.1429 | 65.7702 | 119 | 59 | 122 | 18 | 18 | 100.0000 | |
| ciseli-custom | SNP | * | map_l150_m1_e0 | het | 72.7287 | 66.8410 | 79.7539 | 83.7508 | 12911 | 6405 | 12897 | 3274 | 108 | 3.2987 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.4159 | 66.8404 | 97.8199 | 66.1276 | 4489 | 2227 | 4487 | 100 | 23 | 23.0000 | |
| anovak-vg | INDEL | * | map_l100_m2_e1 | het | 70.6838 | 66.8374 | 75.0000 | 86.9385 | 1566 | 777 | 1653 | 551 | 156 | 28.3122 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 70.6515 | 66.8199 | 74.9493 | 62.1061 | 727 | 361 | 739 | 247 | 164 | 66.3968 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m2_e0 | het | 64.4414 | 66.8008 | 62.2430 | 89.2549 | 332 | 165 | 333 | 202 | 174 | 86.1386 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | hetalt | 79.5048 | 66.7941 | 98.1900 | 36.1641 | 1398 | 695 | 1085 | 20 | 16 | 80.0000 | |
| qzeng-custom | INDEL | I16_PLUS | * | hetalt | 79.3637 | 66.7779 | 97.7954 | 49.1480 | 1401 | 697 | 1109 | 25 | 20 | 80.0000 | |
| asubramanian-gatk | SNP | ti | map_siren | het | 80.0204 | 66.7709 | 99.8298 | 71.1364 | 41653 | 20729 | 41647 | 71 | 23 | 32.3944 | |
| ckim-isaac | SNP | ti | map_l100_m1_e0 | * | 80.0185 | 66.7647 | 99.8378 | 62.0110 | 32001 | 15930 | 32005 | 52 | 10 | 19.2308 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 80.0060 | 66.7485 | 99.8350 | 38.5707 | 2447 | 1219 | 2420 | 4 | 4 | 100.0000 | |
| ckim-gatk | SNP | tv | map_l125_m0_e0 | het | 78.5920 | 66.7348 | 95.5729 | 91.8237 | 2937 | 1464 | 2936 | 136 | 8 | 5.8824 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 70.9466 | 66.7041 | 75.7654 | 53.5142 | 10704 | 5343 | 10864 | 3475 | 3422 | 98.4748 | |