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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43951-44000 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 84.0467 | 75.5245 | 94.7368 | 93.3255 | 108 | 35 | 108 | 6 | 1 | 16.6667 | |
| ckim-isaac | INDEL | * | map_siren | * | 85.3582 | 75.5331 | 98.1215 | 78.4772 | 5597 | 1813 | 5589 | 107 | 46 | 42.9907 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e0 | * | 81.1136 | 75.5435 | 87.5706 | 97.8091 | 139 | 45 | 155 | 22 | 5 | 22.7273 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 84.7019 | 75.5446 | 96.3855 | 35.1952 | 5202 | 1684 | 5200 | 195 | 193 | 98.9744 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.0894 | 75.5459 | 97.3929 | 69.1734 | 519 | 168 | 523 | 14 | 12 | 85.7143 | |
| gduggal-snapplat | INDEL | I1_5 | map_l250_m2_e0 | homalt | 85.0304 | 75.5556 | 97.2222 | 97.5121 | 34 | 11 | 35 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e1 | hetalt | 83.9506 | 75.5556 | 94.4444 | 88.0795 | 34 | 11 | 34 | 2 | 2 | 100.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.0006 | 75.5556 | 92.0732 | 84.2949 | 544 | 176 | 604 | 52 | 4 | 7.6923 | |
| egarrison-hhga | INDEL | D16_PLUS | map_l100_m2_e0 | * | 78.7116 | 75.5556 | 82.1429 | 87.8613 | 68 | 22 | 69 | 15 | 11 | 73.3333 | |
| qzeng-custom | INDEL | I6_15 | segdup | hetalt | 86.0759 | 75.5556 | 100.0000 | 90.9091 | 34 | 11 | 20 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | map_l100_m2_e1 | het | 75.1170 | 75.5556 | 74.6835 | 86.0301 | 102 | 33 | 118 | 40 | 23 | 57.5000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.5043 | 75.5582 | 88.4663 | 84.8513 | 643 | 208 | 721 | 94 | 7 | 7.4468 | |
| qzeng-custom | SNP | tv | map_l125_m2_e1 | * | 85.1190 | 75.5598 | 97.4472 | 83.5794 | 12586 | 4071 | 12559 | 329 | 276 | 83.8906 | |
| ciseli-custom | SNP | tv | map_l250_m2_e0 | homalt | 78.7009 | 75.5603 | 82.1138 | 88.5597 | 708 | 229 | 707 | 154 | 111 | 72.0779 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 84.1998 | 75.5674 | 95.0586 | 89.6740 | 1132 | 366 | 1135 | 59 | 25 | 42.3729 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.9189 | 75.5734 | 99.5461 | 25.8137 | 659 | 213 | 658 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 86.0332 | 75.5734 | 99.8536 | 26.3215 | 659 | 213 | 682 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | * | hetalt | 85.2525 | 75.5818 | 97.7610 | 47.7759 | 6463 | 2088 | 6462 | 148 | 138 | 93.2432 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 47.7941 | 75.5844 | 34.9456 | 64.9725 | 291 | 94 | 289 | 538 | 478 | 88.8476 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 82.5216 | 75.5967 | 90.8430 | 68.5420 | 2692 | 869 | 2748 | 277 | 196 | 70.7581 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.1111 | 75.6098 | 100.0000 | 91.5254 | 31 | 10 | 30 | 0 | 0 | ||
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 77.5000 | 75.6098 | 79.4872 | 90.6475 | 31 | 10 | 31 | 8 | 5 | 62.5000 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 84.9315 | 75.6098 | 96.8750 | 91.1602 | 31 | 10 | 31 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 79.7260 | 75.6106 | 84.3152 | 58.0080 | 4458 | 1438 | 2204 | 410 | 248 | 60.4878 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 79.7260 | 75.6106 | 84.3152 | 58.0080 | 4458 | 1438 | 2204 | 410 | 248 | 60.4878 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 85.6175 | 75.6148 | 98.6702 | 63.9501 | 369 | 119 | 371 | 5 | 3 | 60.0000 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | * | 82.4804 | 75.6151 | 90.7168 | 64.6037 | 9343 | 3013 | 9391 | 961 | 822 | 85.5359 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m2_e0 | homalt | 85.4395 | 75.6198 | 98.1900 | 87.8035 | 183 | 59 | 217 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | INDEL | * | map_l125_m2_e0 | homalt | 84.9635 | 75.6225 | 96.9372 | 90.0183 | 577 | 186 | 633 | 20 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002compoundhet | hetalt | 85.9482 | 75.6238 | 99.5374 | 35.2988 | 6456 | 2081 | 6455 | 30 | 20 | 66.6667 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 85.3226 | 75.6324 | 97.8608 | 79.5261 | 71434 | 23015 | 71409 | 1561 | 832 | 53.2992 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 64.5916 | 75.6355 | 56.3620 | 56.7025 | 1220 | 393 | 1227 | 950 | 942 | 99.1579 | |
| eyeh-varpipe | INDEL | D16_PLUS | map_siren | het | 77.8836 | 75.6410 | 80.2632 | 78.7709 | 59 | 19 | 61 | 15 | 15 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 85.3906 | 75.6471 | 98.0153 | 59.9388 | 643 | 207 | 642 | 13 | 11 | 84.6154 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 79.4494 | 75.6494 | 83.6513 | 75.4184 | 1631 | 525 | 1929 | 377 | 321 | 85.1459 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.8342 | 75.6494 | 91.5271 | 45.0163 | 932 | 300 | 929 | 86 | 62 | 72.0930 | |
| astatham-gatk | SNP | ti | map_l150_m1_e0 | het | 85.9873 | 75.6508 | 99.5954 | 82.9552 | 9358 | 3012 | 9354 | 38 | 18 | 47.3684 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | * | 82.3584 | 75.6514 | 90.3704 | 28.6893 | 1771 | 570 | 1952 | 208 | 208 | 100.0000 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 26.2348 | 75.6579 | 15.8687 | 80.7530 | 115 | 37 | 116 | 615 | 18 | 2.9268 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.2919 | 75.6705 | 97.7165 | 64.9393 | 8690 | 2794 | 8687 | 203 | 174 | 85.7143 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 81.4567 | 75.6715 | 88.1998 | 59.8076 | 12143 | 3904 | 12273 | 1642 | 1435 | 87.3934 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 83.3906 | 75.6757 | 92.8571 | 77.4194 | 28 | 9 | 39 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 85.6972 | 75.6757 | 98.7780 | 69.6726 | 504 | 162 | 485 | 6 | 1 | 16.6667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 85.6972 | 75.6757 | 98.7780 | 69.6726 | 504 | 162 | 485 | 6 | 1 | 16.6667 | |
| gduggal-snapfb | INDEL | D6_15 | map_l125_m2_e1 | homalt | 82.3529 | 75.6757 | 90.3226 | 90.4615 | 28 | 9 | 28 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e1 | * | 81.2198 | 75.6757 | 87.6404 | 97.8476 | 140 | 45 | 156 | 22 | 5 | 22.7273 | |
| astatham-gatk | SNP | ti | map_l150_m2_e1 | het | 86.0111 | 75.6819 | 99.6055 | 83.9600 | 9850 | 3165 | 9846 | 39 | 19 | 48.7179 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 84.8964 | 75.6945 | 96.6451 | 41.6459 | 7929 | 2546 | 7922 | 275 | 269 | 97.8182 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 85.9606 | 75.6948 | 99.4477 | 36.9246 | 2669 | 857 | 2521 | 14 | 12 | 85.7143 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 85.9606 | 75.6948 | 99.4477 | 36.9246 | 2669 | 857 | 2521 | 14 | 12 | 85.7143 | |