PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1251-1300 / 86044 show all | |||||||||||||||
| jmaeng-gatk | SNP | * | map_l125_m1_e0 | homalt | 76.7144 | 62.2360 | 99.9715 | 73.5225 | 10521 | 6384 | 10521 | 3 | 3 | 100.0000 | |
| qzeng-custom | SNP | tv | map_siren | * | 92.0283 | 86.1093 | 98.8212 | 67.3017 | 39550 | 6380 | 39401 | 470 | 339 | 72.1277 | |
| gduggal-snapplat | INDEL | I16_PLUS | * | * | 0.0000 | 0.0157 | 0.0000 | 0.0000 | 1 | 6376 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I16_PLUS | * | * | 0.0000 | 0.0314 | 0.0000 | 0.0000 | 2 | 6375 | 0 | 0 | 0 | ||
| qzeng-custom | SNP | ti | map_l100_m2_e0 | het | 87.5433 | 79.2078 | 97.8395 | 80.9563 | 24255 | 6367 | 24137 | 533 | 415 | 77.8612 | |
| qzeng-custom | SNP | ti | map_l150_m1_e0 | * | 79.6789 | 67.7202 | 96.7669 | 86.5194 | 13349 | 6363 | 13259 | 443 | 380 | 85.7788 | |
| gduggal-snapvard | INDEL | D16_PLUS | * | * | 10.7850 | 6.2058 | 41.1492 | 71.3717 | 421 | 6363 | 444 | 635 | 373 | 58.7402 | |
| asubramanian-gatk | SNP | ti | map_l150_m0_e0 | * | 32.0231 | 19.0688 | 99.8668 | 96.6434 | 1499 | 6362 | 1499 | 2 | 2 | 100.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 57.2983 | 42.6638 | 87.2144 | 64.2116 | 4728 | 6354 | 4543 | 666 | 344 | 51.6517 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | het | 97.0873 | 95.7892 | 98.4210 | 25.5027 | 144384 | 6347 | 144674 | 2321 | 283 | 12.1930 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.1642 | 83.2621 | 85.0860 | 71.1301 | 31558 | 6344 | 32017 | 5612 | 5145 | 91.6785 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e1 | * | 81.2473 | 69.4542 | 97.8644 | 88.4201 | 14393 | 6330 | 14389 | 314 | 34 | 10.8280 | |
| qzeng-custom | SNP | ti | map_l100_m1_e0 | het | 87.3398 | 78.8625 | 97.8592 | 80.1613 | 23613 | 6329 | 23496 | 514 | 414 | 80.5447 | |
| ckim-gatk | SNP | ti | map_l150_m2_e1 | * | 81.3077 | 69.4784 | 97.9917 | 88.2788 | 14398 | 6325 | 14394 | 295 | 35 | 11.8644 | |
| asubramanian-gatk | SNP | * | map_l150_m0_e0 | het | 34.0434 | 20.5290 | 99.6333 | 97.2059 | 1630 | 6310 | 1630 | 6 | 3 | 50.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 89.0223 | 86.9300 | 91.2178 | 68.3628 | 41962 | 6309 | 53834 | 5183 | 1886 | 36.3882 | |
| gduggal-snapvard | INDEL | I16_PLUS | * | * | 2.3476 | 1.2075 | 42.0851 | 50.8200 | 77 | 6300 | 1098 | 1511 | 872 | 57.7101 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e0 | * | 81.1449 | 69.3009 | 97.8719 | 88.3988 | 14215 | 6297 | 14211 | 309 | 34 | 11.0032 | |
| ckim-gatk | SNP | ti | map_l150_m2_e0 | * | 81.1968 | 69.3155 | 97.9938 | 88.2579 | 14218 | 6294 | 14214 | 291 | 35 | 12.0275 | |
| mlin-fermikit | SNP | tv | map_l150_m1_e0 | * | 56.0020 | 42.3295 | 82.7209 | 62.1223 | 4619 | 6293 | 4615 | 964 | 841 | 87.2407 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | * | 36.3679 | 28.3500 | 50.7094 | 30.4777 | 2488 | 6288 | 2502 | 2432 | 2425 | 99.7122 | |
| ckim-isaac | INDEL | * | HG002compoundhet | * | 82.5676 | 79.0154 | 86.4543 | 46.0363 | 23673 | 6287 | 22964 | 3598 | 3236 | 89.9389 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | homalt | 63.8200 | 46.8842 | 99.9099 | 70.9059 | 5545 | 6282 | 5545 | 5 | 5 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.2914 | 83.4336 | 85.1671 | 70.9828 | 31623 | 6279 | 32286 | 5623 | 5042 | 89.6674 | |
| eyeh-varpipe | INDEL | I1_5 | * | hetalt | 60.5783 | 43.9661 | 97.3679 | 73.2444 | 4922 | 6273 | 5216 | 141 | 132 | 93.6170 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 56.5909 | 40.1432 | 95.8723 | 58.5392 | 4205 | 6270 | 6759 | 291 | 284 | 97.5945 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 61.2290 | 64.8241 | 58.0117 | 44.0961 | 11551 | 6268 | 20937 | 15154 | 11698 | 77.1941 | |
| eyeh-varpipe | INDEL | I1_5 | HG002compoundhet | hetalt | 60.8513 | 43.9832 | 98.7067 | 61.4827 | 4916 | 6261 | 5190 | 68 | 65 | 95.5882 | |
| gduggal-bwaplat | SNP | * | map_l125_m0_e0 | het | 67.0117 | 50.6238 | 99.0887 | 93.0436 | 6411 | 6253 | 6415 | 59 | 19 | 32.2034 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 88.2228 | 79.6951 | 98.7942 | 76.5609 | 24515 | 6246 | 24497 | 299 | 252 | 84.2809 | |
| jmaeng-gatk | SNP | ti | map_l150_m1_e0 | * | 80.4694 | 68.3289 | 97.8561 | 87.7017 | 13469 | 6243 | 13465 | 295 | 34 | 11.5254 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 36.9719 | 33.9924 | 40.5239 | 46.0310 | 3215 | 6243 | 3218 | 4723 | 4680 | 99.0896 | |
| ckim-gatk | SNP | ti | map_l150_m1_e0 | * | 80.5127 | 68.3289 | 97.9843 | 87.5524 | 13469 | 6243 | 13465 | 277 | 34 | 12.2744 | |
| asubramanian-gatk | SNP | ti | map_l125_m0_e0 | het | 39.3510 | 24.5068 | 99.8029 | 95.3774 | 2025 | 6238 | 2025 | 4 | 4 | 100.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 76.1646 | 71.9865 | 80.8576 | 48.0795 | 16017 | 6233 | 16537 | 3915 | 3818 | 97.5223 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.9743 | 90.3292 | 93.6805 | 71.4710 | 58200 | 6231 | 60215 | 4062 | 3944 | 97.0950 | |
| ckim-gatk | SNP | * | HG002complexvar | * | 99.5695 | 99.1746 | 99.9675 | 19.4723 | 748154 | 6227 | 748002 | 243 | 101 | 41.5638 | |
| ckim-isaac | SNP | * | map_l150_m2_e0 | homalt | 63.7998 | 46.8587 | 99.9271 | 70.9027 | 5482 | 6217 | 5482 | 4 | 4 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.2088 | 43.9090 | 51.0447 | 54.2294 | 4866 | 6216 | 4886 | 4686 | 4047 | 86.3636 | |
| gduggal-snapplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.8609 | 77.5453 | 93.7004 | 78.4378 | 21463 | 6215 | 21508 | 1446 | 158 | 10.9267 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 49.4570 | 43.9271 | 56.5797 | 43.4855 | 4868 | 6214 | 5009 | 3844 | 2967 | 77.1852 | |
| gduggal-snapfb | INDEL | I1_5 | * | * | 94.6996 | 95.8769 | 93.5508 | 58.0186 | 144452 | 6212 | 145507 | 10031 | 3046 | 30.3659 | |
| gduggal-snapplat | SNP | tv | * | homalt | 99.0993 | 98.3541 | 99.8560 | 22.6563 | 370916 | 6207 | 370887 | 535 | 142 | 26.5421 | |
| eyeh-varpipe | INDEL | I6_15 | * | hetalt | 42.6506 | 27.4354 | 95.7540 | 48.5714 | 2346 | 6205 | 2413 | 107 | 106 | 99.0654 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 71.4050 | 68.7947 | 74.2213 | 55.0266 | 13664 | 6198 | 13653 | 4742 | 4639 | 97.8279 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | hetalt | 42.7960 | 27.4218 | 97.4089 | 29.0841 | 2341 | 6196 | 2406 | 64 | 63 | 98.4375 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 77.1235 | 65.2618 | 94.2549 | 80.4969 | 11629 | 6190 | 11632 | 709 | 196 | 27.6446 | |
| gduggal-bwaplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.9355 | 77.6393 | 98.7607 | 75.1429 | 21489 | 6189 | 21517 | 270 | 69 | 25.5556 | |
| mlin-fermikit | INDEL | * | * | het | 96.2161 | 96.8146 | 95.6251 | 53.1659 | 187949 | 6184 | 187516 | 8579 | 8282 | 96.5381 | |
| ckim-vqsr | SNP | ti | HG002complexvar | homalt | 98.3712 | 96.8046 | 99.9893 | 18.7775 | 187281 | 6182 | 187271 | 20 | 20 | 100.0000 | |