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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40451-40500 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 77.7525 | 64.8746 | 97.0093 | 45.7404 | 181 | 98 | 519 | 16 | 13 | 81.2500 | |
| qzeng-custom | SNP | ti | map_l125_m0_e0 | het | 76.7738 | 64.8796 | 94.0081 | 91.3630 | 5361 | 2902 | 5350 | 341 | 285 | 83.5777 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m2_e0 | het | 63.7616 | 64.8855 | 62.6761 | 90.4313 | 85 | 46 | 89 | 53 | 13 | 24.5283 | |
| ckim-vqsr | SNP | * | map_l150_m2_e1 | het | 78.2150 | 64.9020 | 98.3989 | 91.7124 | 13216 | 7147 | 13213 | 215 | 2 | 0.9302 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 64.9109 | 100.0000 | 838 | 453 | 0 | 0 | 0 | ||||
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 78.3577 | 64.9123 | 98.8281 | 48.0730 | 259 | 140 | 253 | 3 | 3 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 70.3015 | 64.9123 | 76.6667 | 98.8432 | 37 | 20 | 69 | 21 | 16 | 76.1905 | |
| ckim-isaac | SNP | ti | map_l100_m0_e0 | het | 78.6364 | 64.9145 | 99.7144 | 71.0617 | 9077 | 4906 | 9078 | 26 | 3 | 11.5385 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 77.7114 | 64.9157 | 96.7899 | 84.6384 | 1001 | 541 | 995 | 33 | 12 | 36.3636 | |
| gduggal-snapfb | INDEL | D6_15 | HG002complexvar | * | 75.6069 | 64.9189 | 90.5077 | 47.3259 | 3442 | 1860 | 3423 | 359 | 338 | 94.1504 | |
| ckim-isaac | SNP | ti | map_l125_m2_e1 | het | 78.6508 | 64.9290 | 99.7264 | 75.0040 | 12393 | 6694 | 12393 | 34 | 3 | 8.8235 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 74.5911 | 64.9460 | 87.6005 | 39.3454 | 5234 | 2825 | 763 | 108 | 107 | 99.0741 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 74.5911 | 64.9460 | 87.6005 | 39.3454 | 5234 | 2825 | 763 | 108 | 107 | 99.0741 | |
| gduggal-bwavard | INDEL | I6_15 | HG002complexvar | * | 69.2732 | 64.9624 | 74.1967 | 53.0461 | 3113 | 1679 | 3048 | 1060 | 990 | 93.3962 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.3379 | 64.9675 | 95.5272 | 85.0988 | 599 | 323 | 598 | 28 | 8 | 28.5714 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 78.0231 | 64.9737 | 97.6316 | 49.3333 | 371 | 200 | 371 | 9 | 8 | 88.8889 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.8144 | 64.9791 | 93.9211 | 77.3415 | 9498 | 5119 | 9502 | 615 | 178 | 28.9431 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e0 | het | 78.3377 | 64.9794 | 98.6095 | 91.3777 | 8370 | 4511 | 8368 | 118 | 2 | 1.6949 | |
| ckim-isaac | INDEL | * | map_l125_m2_e0 | * | 78.3417 | 64.9818 | 98.6169 | 88.3010 | 1427 | 769 | 1426 | 20 | 8 | 40.0000 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m2_e1 | het | 63.3474 | 64.9842 | 61.7910 | 92.1527 | 206 | 111 | 207 | 128 | 110 | 85.9375 | |
| gduggal-snapfb | INDEL | D6_15 | map_l125_m2_e1 | hetalt | 78.7879 | 65.0000 | 100.0000 | 85.0000 | 13 | 7 | 3 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | map_l150_m0_e0 | het | 77.1875 | 65.0000 | 95.0000 | 85.9155 | 13 | 7 | 19 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 78.7879 | 65.0000 | 100.0000 | 60.6061 | 13 | 7 | 13 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 78.7879 | 65.0000 | 100.0000 | 89.2265 | 39 | 21 | 39 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 72.2222 | 65.0000 | 81.2500 | 99.5143 | 13 | 7 | 13 | 3 | 2 | 66.6667 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 65.0000 | 65.0000 | 65.0000 | 99.6383 | 13 | 7 | 13 | 7 | 5 | 71.4286 | |
| mlin-fermikit | INDEL | D6_15 | map_l125_m2_e1 | hetalt | 76.4706 | 65.0000 | 92.8571 | 75.0000 | 13 | 7 | 13 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l250_m1_e0 | het | 78.7879 | 65.0000 | 100.0000 | 97.5549 | 39 | 21 | 39 | 0 | 0 | ||
| anovak-vg | INDEL | D16_PLUS | map_l125_m1_e0 | het | 70.2703 | 65.0000 | 76.4706 | 88.5135 | 13 | 7 | 13 | 4 | 3 | 75.0000 | |
| anovak-vg | INDEL | D16_PLUS | map_l125_m2_e0 | het | 70.8171 | 65.0000 | 77.7778 | 88.4615 | 13 | 7 | 14 | 4 | 3 | 75.0000 | |
| anovak-vg | INDEL | D16_PLUS | map_l125_m2_e1 | het | 70.8171 | 65.0000 | 77.7778 | 88.6792 | 13 | 7 | 14 | 4 | 3 | 75.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 66.0556 | 65.0014 | 67.1446 | 72.1458 | 2355 | 1268 | 3278 | 1604 | 1089 | 67.8928 | |
| ckim-isaac | INDEL | * | map_l100_m0_e0 | * | 78.2134 | 65.0032 | 98.1625 | 86.3822 | 1016 | 547 | 1015 | 19 | 7 | 36.8421 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.4367 | 65.0167 | 84.3621 | 45.9065 | 1366 | 735 | 1845 | 342 | 338 | 98.8304 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-bwaplat | INDEL | I16_PLUS | HG002compoundhet | hetalt | 78.6021 | 65.0263 | 99.3421 | 43.5644 | 1361 | 732 | 1359 | 9 | 8 | 88.8889 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 55.0866 | 65.0355 | 47.7778 | 51.5804 | 917 | 493 | 1376 | 1504 | 1123 | 74.6676 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 66.3810 | 65.0448 | 67.7731 | 41.7349 | 15962 | 8578 | 15905 | 7563 | 5364 | 70.9242 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 75.3208 | 65.0467 | 89.4493 | 64.1933 | 2088 | 1122 | 2128 | 251 | 224 | 89.2430 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e1 | het | 78.3815 | 65.0480 | 98.5906 | 91.4083 | 8466 | 4549 | 8464 | 121 | 2 | 1.6529 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.3660 | 65.0485 | 98.5401 | 58.3587 | 134 | 72 | 135 | 2 | 1 | 50.0000 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | het | 71.3414 | 65.0579 | 78.9685 | 85.0033 | 4718 | 2534 | 4716 | 1256 | 50 | 3.9809 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 78.3260 | 65.0602 | 98.3871 | 30.3371 | 54 | 29 | 61 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | hetalt | 78.3575 | 65.0620 | 98.4827 | 54.0810 | 1365 | 733 | 1363 | 21 | 19 | 90.4762 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 78.1128 | 65.0730 | 97.6884 | 78.4680 | 3253 | 1746 | 3254 | 77 | 59 | 76.6234 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 78.1128 | 65.0730 | 97.6884 | 78.4680 | 3253 | 1746 | 3254 | 77 | 59 | 76.6234 | |
| ckim-isaac | INDEL | * | map_l125_m2_e1 | * | 78.4183 | 65.0787 | 98.6367 | 88.3507 | 1448 | 777 | 1447 | 20 | 8 | 40.0000 | |