PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
48451-48500 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | * | map_l100_m2_e0 | het | 96.1235 | 98.1795 | 94.1518 | 90.6489 | 2265 | 42 | 2270 | 141 | 14 | 9.9291 | |
| astatham-gatk | INDEL | * | map_l250_m2_e1 | * | 95.4074 | 96.6967 | 94.1520 | 96.3590 | 322 | 11 | 322 | 20 | 4 | 20.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m1_e0 | homalt | 86.3828 | 79.7980 | 94.1520 | 92.3181 | 158 | 40 | 161 | 10 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | * | homalt | 95.9125 | 97.7395 | 94.1526 | 53.1263 | 6183 | 143 | 6183 | 384 | 166 | 43.2292 | |
| asubramanian-gatk | INDEL | * | map_l125_m0_e0 | * | 91.5650 | 89.1156 | 94.1527 | 97.5656 | 786 | 96 | 789 | 49 | 3 | 6.1225 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.2193 | 94.2819 | 94.1567 | 58.3748 | 709 | 43 | 709 | 44 | 28 | 63.6364 | |
| cchapple-custom | SNP | * | map_l150_m0_e0 | het | 94.9871 | 95.8312 | 94.1577 | 84.6817 | 7609 | 331 | 7607 | 472 | 119 | 25.2119 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.4668 | 92.7820 | 94.1618 | 66.2439 | 617 | 48 | 1629 | 101 | 95 | 94.0594 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.4955 | 96.8668 | 94.1624 | 79.5749 | 371 | 12 | 371 | 23 | 18 | 78.2609 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m0_e0 | het | 95.6215 | 97.1235 | 94.1653 | 84.4545 | 574 | 17 | 581 | 36 | 4 | 11.1111 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m1_e0 | * | 93.9837 | 93.8013 | 94.1667 | 85.5706 | 1256 | 83 | 1243 | 77 | 36 | 46.7532 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.4592 | 94.7518 | 94.1685 | 74.3063 | 1336 | 74 | 1308 | 81 | 70 | 86.4198 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m0_e0 | het | 96.2697 | 98.4663 | 94.1691 | 91.3906 | 321 | 5 | 323 | 20 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.3979 | 96.6584 | 94.1699 | 79.6348 | 3905 | 135 | 3602 | 223 | 191 | 85.6502 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 94.2467 | 94.3223 | 94.1712 | 78.1883 | 515 | 31 | 517 | 32 | 11 | 34.3750 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.5017 | 90.8883 | 94.1735 | 55.0486 | 3571 | 358 | 3572 | 221 | 201 | 90.9502 | |
| qzeng-custom | INDEL | I1_5 | map_l250_m2_e1 | * | 70.3456 | 56.1404 | 94.1748 | 98.0570 | 64 | 50 | 97 | 6 | 4 | 66.6667 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m0_e0 | * | 92.6956 | 91.2621 | 94.1748 | 88.1609 | 94 | 9 | 97 | 6 | 2 | 33.3333 | |
| ghariani-varprowl | SNP | * | map_l125_m0_e0 | het | 96.3272 | 98.5786 | 94.1762 | 82.3918 | 12484 | 180 | 12484 | 772 | 162 | 20.9845 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.6354 | 91.1441 | 94.1762 | 35.9848 | 16642 | 1617 | 17303 | 1070 | 870 | 81.3084 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.3319 | 98.5866 | 94.1781 | 59.8901 | 279 | 4 | 275 | 17 | 17 | 100.0000 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | hetalt | 65.3629 | 50.0494 | 94.1788 | 58.1739 | 507 | 506 | 453 | 28 | 24 | 85.7143 | |
| ckim-dragen | INDEL | D1_5 | map_l250_m2_e1 | * | 95.4509 | 96.7568 | 94.1799 | 95.8498 | 179 | 6 | 178 | 11 | 2 | 18.1818 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.5170 | 90.9118 | 94.1799 | 42.0147 | 6072 | 607 | 10761 | 665 | 217 | 32.6316 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.8755 | 85.9451 | 94.1826 | 54.7512 | 56166 | 9185 | 55450 | 3425 | 2525 | 73.7226 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.8755 | 85.9451 | 94.1826 | 54.7512 | 56166 | 9185 | 55450 | 3425 | 2525 | 73.7226 | |
| asubramanian-gatk | INDEL | D1_5 | map_l150_m2_e1 | * | 90.5975 | 87.2751 | 94.1828 | 92.0590 | 679 | 99 | 680 | 42 | 5 | 11.9048 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 94.2194 | 94.2529 | 94.1860 | 99.8927 | 82 | 5 | 81 | 5 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | het | 95.3743 | 96.5928 | 94.1860 | 94.0596 | 567 | 20 | 567 | 35 | 1 | 2.8571 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 50.0731 | 34.1014 | 94.1860 | 56.1224 | 74 | 143 | 81 | 5 | 5 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 80.3116 | 70.0000 | 94.1860 | 83.6812 | 42 | 18 | 81 | 5 | 4 | 80.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.1757 | 96.1815 | 94.1907 | 88.8007 | 2544 | 101 | 2578 | 159 | 6 | 3.7736 | |
| jpowers-varprowl | SNP | tv | map_l125_m0_e0 | het | 94.8319 | 95.4783 | 94.1941 | 83.6101 | 4202 | 199 | 4202 | 259 | 65 | 25.0965 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.5134 | 94.8347 | 94.1942 | 82.6140 | 918 | 50 | 941 | 58 | 19 | 32.7586 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4962 | 98.9130 | 94.1946 | 61.4016 | 1729 | 19 | 1655 | 102 | 27 | 26.4706 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m0_e0 | het | 96.2238 | 98.3333 | 94.2029 | 88.3051 | 59 | 1 | 65 | 4 | 1 | 25.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.0149 | 100.0000 | 94.2029 | 85.9470 | 2 | 0 | 65 | 4 | 3 | 75.0000 | |
| gduggal-snapfb | INDEL | D6_15 | map_l125_m1_e0 | het | 85.4139 | 78.1250 | 94.2029 | 79.5252 | 50 | 14 | 65 | 4 | 3 | 75.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 63.8821 | 48.3271 | 94.2029 | 88.6792 | 130 | 139 | 130 | 8 | 2 | 25.0000 | |
| jpowers-varprowl | INDEL | I6_15 | map_siren | homalt | 81.7610 | 72.2222 | 94.2029 | 75.1799 | 65 | 25 | 65 | 4 | 3 | 75.0000 | |
| ltrigg-rtg2 | INDEL | C16_PLUS | HG002complexvar | * | 0.0000 | 0.0000 | 94.2029 | 89.5928 | 0 | 0 | 65 | 4 | 3 | 75.0000 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m0_e0 | het | 95.1124 | 96.0396 | 94.2029 | 92.3248 | 194 | 8 | 195 | 12 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5538 | 96.9440 | 94.2029 | 48.6379 | 1142 | 36 | 3055 | 188 | 176 | 93.6170 | |
| ghariani-varprowl | INDEL | I6_15 | map_siren | homalt | 81.7610 | 72.2222 | 94.2029 | 76.1246 | 65 | 25 | 65 | 4 | 3 | 75.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 85.4215 | 78.1353 | 94.2062 | 35.5484 | 6386 | 1787 | 2065 | 127 | 67 | 52.7559 | |
| cchapple-custom | INDEL | D6_15 | map_l100_m1_e0 | * | 92.6206 | 91.0853 | 94.2085 | 83.6799 | 235 | 23 | 244 | 15 | 8 | 53.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.8087 | 91.4498 | 94.2085 | 69.3853 | 246 | 23 | 244 | 15 | 7 | 46.6667 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 26.5124 | 15.4269 | 94.2105 | 53.3742 | 365 | 2001 | 358 | 22 | 17 | 77.2727 | |