PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2951-3000 / 86044 show all | |||||||||||||||
| cchapple-custom | SNP | ti | * | * | 99.8773 | 99.8866 | 99.8679 | 19.3368 | 2083147 | 2364 | 2081936 | 2754 | 477 | 17.3203 | |
| gduggal-bwaplat | SNP | tv | map_l150_m1_e0 | homalt | 57.2617 | 40.1166 | 100.0000 | 85.3494 | 1583 | 2363 | 1583 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | map_l250_m1_e0 | het | 33.8831 | 20.4178 | 99.5074 | 98.4836 | 606 | 2362 | 606 | 3 | 1 | 33.3333 | |
| hfeng-pmm1 | SNP | * | * | * | 99.9496 | 99.9227 | 99.9766 | 18.0950 | 3052257 | 2362 | 3052118 | 715 | 107 | 14.9650 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.2959 | 0.0000 | 0.0000 | 7 | 2359 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.2959 | 0.0000 | 0.0000 | 7 | 2359 | 0 | 0 | 0 | ||
| egarrison-hhga | INDEL | * | HG002complexvar | * | 97.4540 | 96.9352 | 97.9784 | 67.1267 | 74580 | 2358 | 74541 | 1538 | 1113 | 72.3667 | |
| gduggal-snapplat | SNP | * | map_l125_m0_e0 | * | 91.0834 | 87.8360 | 94.5802 | 84.8287 | 17027 | 2358 | 17032 | 976 | 546 | 55.9426 | |
| astatham-gatk | SNP | * | map_l125_m0_e0 | het | 89.5045 | 81.3803 | 99.4306 | 82.1625 | 10306 | 2358 | 10303 | 59 | 18 | 30.5085 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 13.4043 | 0.0000 | 0.0000 | 365 | 2358 | 0 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l100_m0_e0 | het | 79.8556 | 67.3775 | 98.0060 | 89.3473 | 4866 | 2356 | 4866 | 99 | 1 | 1.0101 | |
| ckim-isaac | SNP | tv | map_l150_m2_e1 | homalt | 60.1387 | 43.0092 | 99.9438 | 72.5081 | 1778 | 2356 | 1778 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 73.0691 | 85.1079 | 64.0141 | 42.9883 | 13413 | 2347 | 35693 | 20065 | 18085 | 90.1321 | |
| jmaeng-gatk | SNP | tv | HG002complexvar | * | 99.5035 | 99.0473 | 99.9639 | 22.5835 | 243807 | 2345 | 243715 | 88 | 31 | 35.2273 | |
| jpowers-varprowl | INDEL | D1_5 | * | het | 92.8158 | 97.3223 | 88.7081 | 61.6875 | 85229 | 2345 | 85221 | 10848 | 10534 | 97.1055 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.1518 | 91.8431 | 92.4625 | 82.8802 | 26370 | 2342 | 26055 | 2124 | 340 | 16.0075 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.1518 | 91.8431 | 92.4625 | 82.8802 | 26370 | 2342 | 26055 | 2124 | 340 | 16.0075 | |
| gduggal-snapplat | INDEL | D16_PLUS | HG002compoundhet | * | 0.0000 | 0.0000 | 0.0000 | 0 | 2341 | 0 | 0 | 0 | |||
| asubramanian-gatk | SNP | ti | map_l150_m0_e0 | homalt | 26.4068 | 15.2119 | 100.0000 | 94.8680 | 420 | 2341 | 420 | 0 | 0 | ||
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 78.1562 | 80.3015 | 76.1225 | 51.8771 | 9535 | 2339 | 9494 | 2978 | 1387 | 46.5749 | |
| gduggal-snapfb | INDEL | D16_PLUS | HG002compoundhet | * | 0.1707 | 0.0854 | 100.0000 | 0.0000 | 2 | 2339 | 1 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | map_l250_m2_e1 | het | 44.9323 | 29.1604 | 97.8637 | 82.7453 | 962 | 2337 | 962 | 21 | 1 | 4.7619 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8694 | 96.4285 | 97.3143 | 66.9705 | 63017 | 2334 | 62795 | 1733 | 1467 | 84.6509 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8694 | 96.4285 | 97.3143 | 66.9705 | 63017 | 2334 | 62795 | 1733 | 1467 | 84.6509 | |
| ciseli-custom | SNP | * | map_l125_m2_e1 | homalt | 88.1920 | 86.6872 | 89.7500 | 68.5967 | 15198 | 2334 | 15148 | 1730 | 1386 | 80.1156 | |
| ckim-isaac | SNP | tv | map_l150_m2_e0 | homalt | 59.9931 | 42.8606 | 99.9429 | 72.5764 | 1750 | 2333 | 1750 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 24.7522 | 14.3959 | 88.2086 | 64.5213 | 392 | 2331 | 389 | 52 | 41 | 78.8462 | |
| ckim-gatk | SNP | tv | map_l125_m2_e1 | homalt | 76.2777 | 61.6727 | 99.9466 | 77.3753 | 3746 | 2328 | 3746 | 2 | 0 | 0.0000 | |
| anovak-vg | SNP | * | map_l100_m0_e0 | het | 78.3081 | 89.0262 | 69.8934 | 77.2580 | 18878 | 2327 | 18693 | 8052 | 2114 | 26.2543 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 89.5071 | 83.4165 | 96.5571 | 49.6329 | 11705 | 2327 | 3113 | 111 | 109 | 98.1982 | |
| jmaeng-gatk | SNP | tv | map_l125_m2_e1 | homalt | 76.3359 | 61.7386 | 99.9733 | 76.6438 | 3750 | 2324 | 3750 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 56.5351 | 42.3182 | 85.1372 | 53.5880 | 1705 | 2324 | 1707 | 298 | 259 | 86.9128 | |
| gduggal-bwafb | INDEL | I6_15 | * | hetalt | 81.7221 | 72.8336 | 93.0818 | 54.0993 | 6228 | 2323 | 1480 | 110 | 109 | 99.0909 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.1346 | 84.9322 | 98.3142 | 43.5277 | 13094 | 2323 | 13472 | 231 | 203 | 87.8788 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 90.4880 | 83.4521 | 98.8195 | 30.8039 | 11710 | 2322 | 12138 | 145 | 128 | 88.2759 | |
| gduggal-bwafb | INDEL | I6_15 | HG002compoundhet | hetalt | 82.7582 | 72.8242 | 95.8306 | 40.7336 | 6217 | 2320 | 1471 | 64 | 63 | 98.4375 | |
| ndellapenna-hhga | INDEL | * | * | het | 97.8590 | 98.8060 | 96.9301 | 56.3967 | 191815 | 2318 | 193328 | 6123 | 5425 | 88.6004 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 83.0248 | 72.2847 | 97.5133 | 68.6969 | 6043 | 2317 | 6039 | 154 | 132 | 85.7143 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 83.0248 | 72.2847 | 97.5133 | 68.6969 | 6043 | 2317 | 6039 | 154 | 132 | 85.7143 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.4166 | 67.7028 | 90.3846 | 37.1872 | 4857 | 2317 | 658 | 70 | 69 | 98.5714 | |
| ckim-gatk | SNP | tv | map_l125_m2_e0 | homalt | 76.1523 | 61.5091 | 99.9460 | 77.4235 | 3701 | 2316 | 3701 | 2 | 0 | 0.0000 | |
| ckim-gatk | SNP | tv | * | het | 99.5973 | 99.6088 | 99.5858 | 30.9441 | 589381 | 2315 | 589308 | 2451 | 61 | 2.4888 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | homalt | 88.1697 | 86.6763 | 89.7155 | 68.5746 | 15060 | 2315 | 15013 | 1721 | 1379 | 80.1278 | |
| cchapple-custom | SNP | * | * | het | 99.7822 | 99.8765 | 99.6880 | 23.4490 | 1871274 | 2313 | 1871921 | 5859 | 675 | 11.5207 | |
| mlin-fermikit | SNP | ti | map_l250_m2_e0 | het | 44.6395 | 28.9183 | 97.8170 | 82.5282 | 941 | 2313 | 941 | 21 | 1 | 4.7619 | |
| mlin-fermikit | SNP | * | map_l150_m0_e0 | homalt | 52.6207 | 43.4581 | 66.6792 | 59.8524 | 1777 | 2312 | 1777 | 888 | 815 | 91.7793 | |
| jmaeng-gatk | SNP | tv | map_l125_m2_e0 | homalt | 76.2110 | 61.5755 | 99.9730 | 76.6962 | 3705 | 2312 | 3705 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 51.7017 | 43.2260 | 64.3120 | 56.8434 | 1758 | 2309 | 1748 | 970 | 697 | 71.8557 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 59.5875 | 61.0924 | 58.1549 | 41.9454 | 3624 | 2308 | 5623 | 4046 | 3831 | 94.6861 | |
| ciseli-custom | SNP | tv | map_l100_m0_e0 | het | 74.3908 | 68.0559 | 82.0260 | 79.9973 | 4915 | 2307 | 4915 | 1077 | 42 | 3.8997 | |