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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39151-39200 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | het | 81.8182 | 90.0000 | 75.0000 | 99.2945 | 9 | 1 | 9 | 3 | 2 | 66.6667 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 81.8182 | 81.8182 | 81.8182 | 99.0886 | 9 | 2 | 9 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D1_5 | map_l125_m1_e0 | hetalt | 81.8182 | 69.2308 | 100.0000 | 96.9388 | 9 | 4 | 9 | 0 | 0 | ||
| ckim-isaac | SNP | * | map_l100_m2_e0 | het | 81.8136 | 69.3420 | 99.7551 | 67.9608 | 32174 | 14225 | 32181 | 79 | 12 | 15.1899 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 81.8133 | 75.2350 | 89.6520 | 58.5736 | 3761 | 1238 | 3942 | 455 | 448 | 98.4615 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 81.8133 | 75.2350 | 89.6520 | 58.5736 | 3761 | 1238 | 3942 | 455 | 448 | 98.4615 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 81.8131 | 80.9524 | 82.6923 | 99.2172 | 34 | 8 | 43 | 9 | 1 | 11.1111 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 81.8128 | 74.8933 | 90.1411 | 58.1664 | 7544 | 2529 | 8942 | 978 | 867 | 88.6503 | |
| anovak-vg | SNP | tv | map_l250_m1_e0 | homalt | 81.8115 | 69.6262 | 99.1667 | 88.3586 | 596 | 260 | 595 | 5 | 3 | 60.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 81.8084 | 94.5910 | 72.0693 | 83.9601 | 1434 | 82 | 1414 | 548 | 14 | 2.5547 | |
| gduggal-snapplat | INDEL | * | map_l125_m0_e0 | homalt | 81.8078 | 70.7746 | 96.9163 | 92.3518 | 201 | 83 | 220 | 7 | 0 | 0.0000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.8034 | 73.8226 | 91.7189 | 86.0200 | 674 | 239 | 731 | 66 | 8 | 12.1212 | |
| ciseli-custom | SNP | ti | map_l125_m1_e0 | * | 81.8023 | 77.7842 | 86.2580 | 75.7269 | 22818 | 6517 | 22798 | 3632 | 966 | 26.5969 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.8009 | 78.9787 | 84.8322 | 50.9671 | 11677 | 3108 | 11678 | 2088 | 2070 | 99.1379 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.7913 | 85.3474 | 78.5196 | 66.0925 | 565 | 97 | 541 | 148 | 141 | 95.2703 | |
| ciseli-custom | INDEL | * | HG002complexvar | homalt | 81.7869 | 88.0268 | 76.3731 | 56.3608 | 23791 | 3236 | 23555 | 7287 | 5323 | 73.0479 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 81.7839 | 72.4138 | 93.9394 | 99.8971 | 63 | 24 | 62 | 4 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 81.7820 | 89.5719 | 75.2387 | 54.8652 | 2448 | 285 | 2443 | 804 | 793 | 98.6318 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 81.7737 | 94.2085 | 72.2388 | 51.3788 | 244 | 15 | 242 | 93 | 93 | 100.0000 | |
| gduggal-bwavard | SNP | tv | HG002compoundhet | het | 81.7704 | 86.9463 | 77.1761 | 55.8414 | 4063 | 610 | 4504 | 1332 | 1169 | 87.7628 | |
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | * | 81.7650 | 70.7957 | 96.7567 | 85.8314 | 7847 | 3237 | 7846 | 263 | 11 | 4.1825 | |
| jpowers-varprowl | INDEL | I6_15 | map_siren | homalt | 81.7610 | 72.2222 | 94.2029 | 75.1799 | 65 | 25 | 65 | 4 | 3 | 75.0000 | |
| ghariani-varprowl | INDEL | I6_15 | map_siren | homalt | 81.7610 | 72.2222 | 94.2029 | 76.1246 | 65 | 25 | 65 | 4 | 3 | 75.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 81.7599 | 69.8795 | 98.5075 | 30.9278 | 58 | 25 | 66 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | HG002compoundhet | * | 81.7565 | 82.9255 | 80.6200 | 31.3934 | 7489 | 1542 | 8582 | 2063 | 963 | 46.6796 | |
| anovak-vg | SNP | tv | map_l250_m2_e0 | homalt | 81.7550 | 69.5838 | 99.0868 | 89.1941 | 652 | 285 | 651 | 6 | 4 | 66.6667 | |
| gduggal-snapplat | INDEL | D1_5 | func_cds | het | 81.7516 | 78.8235 | 84.9057 | 60.5948 | 67 | 18 | 90 | 16 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 81.7466 | 69.7674 | 98.6920 | 34.2284 | 2460 | 1066 | 2490 | 33 | 24 | 72.7273 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 81.7466 | 69.7674 | 98.6920 | 34.2284 | 2460 | 1066 | 2490 | 33 | 24 | 72.7273 | |
| ckim-gatk | SNP | tv | map_l100_m0_e0 | * | 81.7454 | 70.6424 | 96.9896 | 85.6470 | 7830 | 3254 | 7829 | 243 | 11 | 4.5268 | |
| ckim-isaac | INDEL | D1_5 | map_l125_m1_e0 | het | 81.7401 | 69.9725 | 98.2659 | 88.4897 | 508 | 218 | 510 | 9 | 3 | 33.3333 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 81.7400 | 74.7573 | 90.1615 | 62.2924 | 616 | 208 | 614 | 67 | 57 | 85.0746 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m1_e0 | homalt | 81.7391 | 73.4375 | 92.1569 | 88.6414 | 47 | 17 | 47 | 4 | 4 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7362 | 74.1234 | 91.0918 | 40.7803 | 4397 | 1535 | 4397 | 430 | 427 | 99.3023 | |
| qzeng-custom | SNP | * | map_l150_m2_e1 | het | 81.7356 | 71.3795 | 95.6069 | 89.7988 | 14535 | 5828 | 14407 | 662 | 554 | 83.6858 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 81.7356 | 74.1096 | 91.1111 | 54.0230 | 1623 | 567 | 328 | 32 | 32 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 81.7352 | 100.0000 | 69.1120 | 78.6831 | 155 | 0 | 179 | 80 | 5 | 6.2500 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | * | 81.7339 | 69.9161 | 98.3594 | 84.3176 | 2582 | 1111 | 2578 | 43 | 21 | 48.8372 | |
| asubramanian-gatk | INDEL | I6_15 | map_l125_m0_e0 | * | 81.7337 | 73.3333 | 92.3077 | 96.1310 | 11 | 4 | 12 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 81.7312 | 69.6640 | 98.8549 | 64.9750 | 4230 | 1842 | 4230 | 49 | 43 | 87.7551 | |
| mlin-fermikit | INDEL | I6_15 | map_siren | homalt | 81.7259 | 76.6667 | 87.5000 | 82.1029 | 69 | 21 | 70 | 10 | 10 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 81.7248 | 70.3180 | 97.5490 | 56.0345 | 199 | 84 | 199 | 5 | 5 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | * | hetalt | 81.7221 | 72.8336 | 93.0818 | 54.0993 | 6228 | 2323 | 1480 | 110 | 109 | 99.0909 | |
| gduggal-bwavard | INDEL | * | tech_badpromoters | het | 81.7204 | 97.4359 | 70.3704 | 60.0000 | 38 | 1 | 38 | 16 | 15 | 93.7500 | |
| mlin-fermikit | INDEL | I6_15 | map_siren | * | 81.7172 | 75.7377 | 88.7218 | 80.5981 | 231 | 74 | 236 | 30 | 28 | 93.3333 | |
| ckim-isaac | INDEL | * | map_l100_m2_e1 | * | 81.7169 | 69.9148 | 98.3127 | 84.3697 | 2626 | 1130 | 2622 | 45 | 21 | 46.6667 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | * | 81.7142 | 76.1213 | 88.1941 | 27.9899 | 1782 | 559 | 1763 | 236 | 205 | 86.8644 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 81.7107 | 93.5185 | 72.5504 | 85.4033 | 1212 | 84 | 1007 | 381 | 58 | 15.2231 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 81.7047 | 98.6709 | 69.7171 | 59.9362 | 1559 | 21 | 1577 | 685 | 12 | 1.7518 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.7040 | 72.4326 | 93.6973 | 66.4963 | 22281 | 8480 | 22240 | 1496 | 1307 | 87.3663 | |