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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14251-14300 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.6321 | 89.4447 | 85.8915 | 75.4124 | 1627 | 192 | 1869 | 307 | 263 | 85.6678 | |
| ndellapenna-hhga | SNP | * | HG002compoundhet | * | 98.3720 | 97.8158 | 98.9346 | 39.5539 | 25258 | 564 | 25258 | 272 | 233 | 85.6618 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.3979 | 96.6584 | 94.1699 | 79.6348 | 3905 | 135 | 3602 | 223 | 191 | 85.6502 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.1010 | 95.3685 | 92.8667 | 39.9701 | 9925 | 482 | 9699 | 745 | 638 | 85.6376 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| mlin-fermikit | SNP | * | map_siren | * | 83.3638 | 74.6157 | 94.4357 | 47.0930 | 109109 | 37119 | 109094 | 6428 | 5503 | 85.6098 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.9278 | 99.0227 | 93.0204 | 76.6292 | 5370 | 53 | 5371 | 403 | 345 | 85.6079 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.9278 | 99.0227 | 93.0204 | 76.6292 | 5370 | 53 | 5371 | 403 | 345 | 85.6079 | |
| ghariani-varprowl | SNP | tv | HG002compoundhet | homalt | 83.7163 | 99.8524 | 72.0698 | 50.4793 | 3383 | 5 | 3388 | 1313 | 1124 | 85.6055 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.5554 | 89.9881 | 95.2735 | 38.7245 | 28789 | 3203 | 28422 | 1410 | 1207 | 85.6028 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m2_e0 | het | 62.9373 | 64.4013 | 61.5385 | 92.2212 | 199 | 110 | 200 | 125 | 107 | 85.6000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0533 | 97.6374 | 98.4728 | 67.8136 | 63807 | 1544 | 63576 | 986 | 844 | 85.5984 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0533 | 97.6374 | 98.4728 | 67.8136 | 63807 | 1544 | 63576 | 986 | 844 | 85.5984 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.6603 | 29.2554 | 86.0104 | 46.9780 | 1497 | 3620 | 1494 | 243 | 208 | 85.5967 | |
| raldana-dualsentieon | INDEL | * | HG002complexvar | * | 98.9594 | 98.2323 | 99.6974 | 57.2556 | 75578 | 1360 | 75441 | 229 | 196 | 85.5895 | |
| gduggal-bwaplat | INDEL | D1_5 | * | homalt | 94.9240 | 90.7227 | 99.5332 | 62.2451 | 44387 | 4539 | 44353 | 208 | 178 | 85.5769 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | * | 82.4804 | 75.6151 | 90.7168 | 64.6037 | 9343 | 3013 | 9391 | 961 | 822 | 85.5359 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.0676 | 74.4893 | 86.5491 | 57.6750 | 13163 | 4508 | 13345 | 2074 | 1774 | 85.5352 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.0676 | 74.4893 | 86.5491 | 57.6750 | 13163 | 4508 | 13345 | 2074 | 1774 | 85.5352 | |
| rpoplin-dv42 | SNP | ti | HG002complexvar | * | 99.9216 | 99.8731 | 99.9701 | 17.4429 | 507791 | 645 | 507725 | 152 | 130 | 85.5263 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.3526 | 88.8889 | 96.0973 | 56.8254 | 1184 | 148 | 1699 | 69 | 59 | 85.5072 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 48.6065 | 77.8364 | 35.3365 | 53.6490 | 295 | 84 | 294 | 538 | 460 | 85.5019 | |
| jlack-gatk | INDEL | I6_15 | * | * | 96.1308 | 95.2745 | 97.0025 | 53.1865 | 23650 | 1173 | 23656 | 731 | 625 | 85.4993 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 77.1877 | 70.6598 | 85.0445 | 46.2575 | 6683 | 2775 | 6784 | 1193 | 1020 | 85.4987 | |
| gduggal-bwaplat | SNP | ti | * | homalt | 99.0843 | 98.2012 | 99.9834 | 17.0820 | 788593 | 14445 | 788346 | 131 | 112 | 85.4962 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 86.7930 | 84.0381 | 89.7346 | 47.2948 | 2027 | 385 | 6626 | 758 | 648 | 85.4881 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | het | 92.1803 | 94.9412 | 89.5755 | 66.2595 | 807 | 43 | 5740 | 668 | 571 | 85.4790 | |
| qzeng-custom | SNP | * | map_l150_m1_e0 | * | 80.7203 | 69.2737 | 96.6985 | 86.4603 | 21204 | 9405 | 20971 | 716 | 612 | 85.4749 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m2_e0 | homalt | 83.8286 | 85.9247 | 81.8323 | 83.8435 | 525 | 86 | 527 | 117 | 100 | 85.4701 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 5.7971 | 3.3816 | 20.2899 | 80.2292 | 14 | 400 | 14 | 55 | 47 | 85.4545 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.5569 | 94.9365 | 90.2936 | 47.5778 | 11887 | 634 | 11256 | 1210 | 1034 | 85.4545 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 79.7448 | 96.1003 | 68.1467 | 47.3577 | 345 | 14 | 353 | 165 | 141 | 85.4545 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0742 | 96.5582 | 99.6386 | 56.1134 | 30327 | 1081 | 30328 | 110 | 94 | 85.4545 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0742 | 96.5582 | 99.6386 | 56.1134 | 30327 | 1081 | 30328 | 110 | 94 | 85.4545 | |
| jpowers-varprowl | INDEL | * | HG002complexvar | homalt | 94.9661 | 93.9024 | 96.0543 | 47.7714 | 25379 | 1648 | 25269 | 1038 | 887 | 85.4528 | |
| qzeng-custom | SNP | ti | map_l150_m2_e1 | * | 80.4222 | 68.7352 | 96.8977 | 87.0560 | 14244 | 6479 | 14149 | 453 | 387 | 85.4305 | |
| mlin-fermikit | SNP | ti | map_l250_m2_e0 | * | 48.4805 | 33.9257 | 84.9075 | 79.7858 | 1699 | 3309 | 1699 | 302 | 258 | 85.4305 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.7862 | 96.4642 | 95.1177 | 63.6639 | 6193 | 227 | 14027 | 720 | 615 | 85.4167 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.7862 | 96.4642 | 95.1177 | 63.6639 | 6193 | 227 | 14027 | 720 | 615 | 85.4167 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m0_e0 | * | 63.8147 | 51.4113 | 84.1060 | 79.6633 | 255 | 241 | 254 | 48 | 41 | 85.4167 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 80.7906 | 68.5669 | 98.3181 | 40.6653 | 2622 | 1202 | 2806 | 48 | 41 | 85.4167 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.2224 | 98.6702 | 93.8931 | 48.2213 | 742 | 10 | 738 | 48 | 41 | 85.4167 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 66.4101 | 59.5041 | 75.1295 | 58.0435 | 144 | 98 | 145 | 48 | 41 | 85.4167 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 54.4770 | 39.2554 | 88.9798 | 82.4941 | 6052 | 9365 | 6088 | 754 | 644 | 85.4111 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.1782 | 35.9607 | 88.7235 | 60.7545 | 5046 | 8986 | 5067 | 644 | 550 | 85.4037 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | * | 80.3185 | 68.5989 | 96.8676 | 87.0371 | 14071 | 6441 | 13978 | 452 | 386 | 85.3982 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 87.6160 | 82.5603 | 93.3313 | 53.0320 | 3044 | 643 | 3065 | 219 | 187 | 85.3881 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.7603 | 96.7298 | 96.7909 | 69.6486 | 3934 | 133 | 3921 | 130 | 111 | 85.3846 | |