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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13251-13300 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.3059 | 89.5985 | 99.5353 | 25.4660 | 7253 | 842 | 7283 | 34 | 30 | 88.2353 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.2746 | 89.5387 | 99.5395 | 27.7522 | 7318 | 855 | 7349 | 34 | 30 | 88.2353 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1875 | 96.2685 | 98.1242 | 59.9927 | 30236 | 1172 | 30236 | 578 | 510 | 88.2353 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 93.0769 | 99.1803 | 87.6812 | 86.5889 | 121 | 1 | 121 | 17 | 15 | 88.2353 | |
| jlack-gatk | SNP | ti | map_l100_m1_e0 | homalt | 99.3843 | 98.8697 | 99.9044 | 57.5961 | 17757 | 203 | 17757 | 17 | 15 | 88.2353 | |
| jlack-gatk | SNP | ti | map_l100_m2_e0 | homalt | 99.3934 | 98.8858 | 99.9062 | 60.1223 | 18105 | 204 | 18105 | 17 | 15 | 88.2353 | |
| jlack-gatk | SNP | ti | map_l100_m2_e1 | homalt | 99.3913 | 98.8807 | 99.9071 | 60.0864 | 18287 | 207 | 18287 | 17 | 15 | 88.2353 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.3347 | 93.7357 | 96.9893 | 65.2412 | 9442 | 631 | 9310 | 289 | 255 | 88.2353 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9781 | 96.7532 | 97.2039 | 68.0840 | 596 | 20 | 591 | 17 | 15 | 88.2353 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.8101 | 96.4286 | 97.1947 | 67.9535 | 594 | 22 | 589 | 17 | 15 | 88.2353 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7733 | 90.0718 | 97.7922 | 67.5516 | 753 | 83 | 753 | 17 | 15 | 88.2353 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.8400 | 87.9187 | 96.1276 | 66.5396 | 735 | 101 | 844 | 34 | 30 | 88.2353 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.9958 | 80.4949 | 97.0383 | 67.7165 | 553 | 134 | 557 | 17 | 15 | 88.2353 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | homalt | 99.8538 | 99.8679 | 99.8397 | 60.1891 | 10584 | 14 | 10591 | 17 | 15 | 88.2353 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 73.4050 | 58.5620 | 98.3268 | 40.8270 | 1067 | 755 | 999 | 17 | 15 | 88.2353 | |
| egarrison-hhga | SNP | ti | map_siren | homalt | 99.8640 | 99.7732 | 99.9551 | 52.1965 | 37830 | 86 | 37830 | 17 | 15 | 88.2353 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 71.1860 | 58.6207 | 90.6077 | 99.6597 | 51 | 36 | 328 | 34 | 30 | 88.2353 | |
| eyeh-varpipe | INDEL | C6_15 | HG002compoundhet | homalt | 0.0000 | 0.0000 | 2.8571 | 84.2342 | 0 | 0 | 1 | 34 | 30 | 88.2353 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9781 | 96.7532 | 97.2039 | 68.1675 | 596 | 20 | 591 | 17 | 15 | 88.2353 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2925 | 98.9506 | 97.6432 | 71.0801 | 17632 | 187 | 17235 | 416 | 367 | 88.2212 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.9297 | 98.8747 | 93.1551 | 69.8469 | 11422 | 130 | 11432 | 840 | 741 | 88.2143 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.9297 | 98.8747 | 93.1551 | 69.8469 | 11422 | 130 | 11432 | 840 | 741 | 88.2143 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e0 | * | 64.0610 | 50.1091 | 88.7802 | 61.1948 | 15162 | 15096 | 15161 | 1916 | 1690 | 88.2046 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 86.2959 | 82.2171 | 90.8006 | 44.5699 | 3204 | 693 | 7531 | 763 | 673 | 88.2045 | |
| jmaeng-gatk | INDEL | D6_15 | * | * | 97.9970 | 97.6008 | 98.3964 | 55.6203 | 25466 | 626 | 25465 | 415 | 366 | 88.1928 | |
| ckim-isaac | INDEL | I1_5 | * | hetalt | 89.8867 | 82.5636 | 98.6351 | 45.1097 | 9243 | 1952 | 9178 | 127 | 112 | 88.1890 | |
| gduggal-bwaplat | SNP | * | * | homalt | 98.9364 | 97.9135 | 99.9810 | 18.7279 | 1155537 | 24624 | 1155217 | 220 | 194 | 88.1818 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e0 | * | 58.1126 | 43.6427 | 86.9367 | 65.5641 | 8952 | 11560 | 8951 | 1345 | 1186 | 88.1784 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 64.3216 | 84.4327 | 51.9481 | 54.2348 | 320 | 59 | 320 | 296 | 261 | 88.1757 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7273 | 95.9551 | 99.5663 | 48.2367 | 21350 | 900 | 21351 | 93 | 82 | 88.1720 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | homalt | 54.3276 | 66.0194 | 46.1538 | 39.2523 | 204 | 105 | 210 | 245 | 216 | 88.1633 | |
| mlin-fermikit | SNP | tv | map_l250_m1_e0 | * | 43.4641 | 30.3362 | 76.6221 | 76.8295 | 803 | 1844 | 803 | 245 | 216 | 88.1633 | |
| astatham-gatk | SNP | * | * | homalt | 99.9742 | 99.9548 | 99.9936 | 17.1971 | 1179627 | 534 | 1179603 | 76 | 67 | 88.1579 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 53.8527 | 45.9807 | 64.9770 | 74.1667 | 143 | 168 | 141 | 76 | 67 | 88.1579 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.9135 | 97.8996 | 97.9275 | 49.2246 | 3589 | 77 | 3591 | 76 | 67 | 88.1579 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e1 | * | 58.3031 | 43.8450 | 86.9877 | 65.8089 | 9086 | 11637 | 9085 | 1359 | 1198 | 88.1531 | |
| gduggal-bwavard | INDEL | D1_5 | * | het | 93.4417 | 99.0111 | 88.4655 | 62.3753 | 86708 | 866 | 85823 | 11190 | 9864 | 88.1501 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.5227 | 93.4426 | 77.1574 | 75.5280 | 456 | 32 | 456 | 135 | 119 | 88.1481 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.0480 | 87.7443 | 94.6101 | 39.6686 | 12973 | 1812 | 12884 | 734 | 647 | 88.1471 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 80.3927 | 81.2870 | 79.5178 | 59.9939 | 9335 | 2149 | 9333 | 2404 | 2119 | 88.1448 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.8816 | 95.9653 | 93.8220 | 79.5053 | 3877 | 163 | 3584 | 236 | 208 | 88.1356 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8202 | 97.9852 | 99.6695 | 59.8782 | 17800 | 366 | 17792 | 59 | 52 | 88.1356 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8202 | 97.9852 | 99.6695 | 59.8782 | 17800 | 366 | 17792 | 59 | 52 | 88.1356 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | homalt | 98.7666 | 98.4933 | 99.0414 | 43.6510 | 6145 | 94 | 6096 | 59 | 52 | 88.1356 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 62.7608 | 46.6890 | 95.7058 | 37.3301 | 2228 | 2544 | 2251 | 101 | 89 | 88.1188 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e1 | * | 64.3036 | 50.3876 | 88.8389 | 61.3583 | 15403 | 15166 | 15402 | 1935 | 1705 | 88.1137 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.7480 | 95.8991 | 95.5975 | 81.7695 | 912 | 39 | 912 | 42 | 37 | 88.0952 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7046 | 95.7031 | 97.7273 | 60.0519 | 1715 | 77 | 1806 | 42 | 37 | 88.0952 | |