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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3751-3800 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | SNP | * | * | * | 99.9496 | 99.9227 | 99.9766 | 18.0950 | 3052257 | 2362 | 3052118 | 715 | 107 | 14.9650 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 36.4192 | 29.7932 | 46.8354 | 63.9946 | 634 | 1494 | 629 | 714 | 663 | 92.8571 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 77.6220 | 87.0095 | 70.0629 | 67.3332 | 1641 | 245 | 1671 | 714 | 601 | 84.1737 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 44.0199 | 83.7017 | 29.8625 | 62.4216 | 303 | 59 | 304 | 714 | 698 | 97.7591 | |
| ghariani-varprowl | INDEL | D1_5 | HG002compoundhet | homalt | 41.9971 | 92.4399 | 27.1706 | 69.3007 | 269 | 22 | 266 | 713 | 597 | 83.7307 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.5231 | 98.6023 | 94.5298 | 62.0425 | 12346 | 175 | 12304 | 712 | 693 | 97.3315 | |
| ckim-dragen | SNP | tv | map_siren | het | 98.4766 | 99.4128 | 97.5580 | 65.5354 | 28441 | 168 | 28444 | 712 | 52 | 7.3034 | |
| jpowers-varprowl | SNP | * | segdup | het | 97.3794 | 98.7931 | 96.0056 | 92.7629 | 17108 | 209 | 17113 | 712 | 6 | 0.8427 | |
| hfeng-pmm2 | INDEL | * | * | het | 99.3911 | 99.1521 | 99.6313 | 58.9414 | 192487 | 1646 | 192126 | 711 | 412 | 57.9466 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 39.9506 | 39.3669 | 40.5518 | 64.0084 | 485 | 747 | 485 | 711 | 356 | 50.0703 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 79.9918 | 88.3797 | 73.0580 | 45.8556 | 540 | 71 | 1928 | 711 | 372 | 52.3207 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.4578 | 77.0718 | 28.3552 | 59.9110 | 279 | 83 | 281 | 710 | 706 | 99.4366 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 87.2516 | 95.2396 | 80.4999 | 81.9090 | 2941 | 147 | 2931 | 710 | 57 | 8.0282 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 90.7313 | 91.0661 | 90.3989 | 49.5222 | 6116 | 600 | 6685 | 710 | 208 | 29.2958 | |
| gduggal-snapplat | INDEL | * | HG002compoundhet | hetalt | 52.0071 | 36.1279 | 92.7918 | 75.2011 | 9097 | 16083 | 9127 | 709 | 591 | 83.3568 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e1 | het | 96.2073 | 95.9191 | 96.4972 | 82.5948 | 19532 | 831 | 19532 | 709 | 207 | 29.1961 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 77.1235 | 65.2618 | 94.2549 | 80.4969 | 11629 | 6190 | 11632 | 709 | 196 | 27.6446 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 52.1457 | 98.9446 | 35.4015 | 37.2279 | 375 | 4 | 388 | 708 | 669 | 94.4915 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 92.4964 | 96.7963 | 88.5622 | 52.1231 | 5499 | 182 | 5482 | 708 | 693 | 97.8814 | |
| mlin-fermikit | SNP | tv | HG002compoundhet | * | 91.2208 | 90.4965 | 91.9568 | 50.8884 | 8075 | 848 | 8083 | 707 | 593 | 83.8755 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 77.5375 | 77.3507 | 77.7253 | 87.2862 | 2435 | 713 | 2467 | 707 | 54 | 7.6379 | |
| cchapple-custom | INDEL | * | HG002compoundhet | het | 96.8882 | 95.2125 | 98.6240 | 55.6229 | 3898 | 196 | 50675 | 707 | 621 | 87.8359 | |
| ckim-dragen | SNP | ti | map_l125_m2_e1 | * | 98.4185 | 99.1233 | 97.7236 | 74.4858 | 30301 | 268 | 30308 | 706 | 81 | 11.4731 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 82.3435 | 83.6876 | 81.0419 | 74.6270 | 3032 | 591 | 3018 | 706 | 302 | 42.7762 | |
| ciseli-custom | SNP | tv | segdup | * | 95.0488 | 98.0661 | 92.2117 | 92.0351 | 8367 | 165 | 8347 | 705 | 88 | 12.4823 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.1772 | 16.4208 | 39.3809 | 42.5111 | 345 | 1756 | 458 | 705 | 585 | 82.9787 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 79.6213 | 77.5816 | 81.7711 | 43.7436 | 3163 | 914 | 3158 | 704 | 666 | 94.6023 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 89.7564 | 96.6277 | 83.7975 | 65.1703 | 3639 | 127 | 3641 | 704 | 688 | 97.7273 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 89.7564 | 96.6277 | 83.7975 | 65.1703 | 3639 | 127 | 3641 | 704 | 688 | 97.7273 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 71.6758 | 63.5678 | 82.1546 | 59.3969 | 10619 | 6086 | 3241 | 704 | 487 | 69.1761 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 71.6758 | 63.5678 | 82.1546 | 59.3969 | 10619 | 6086 | 3241 | 704 | 487 | 69.1761 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e0 | het | 96.1913 | 95.9023 | 96.4821 | 82.5326 | 19308 | 825 | 19308 | 704 | 206 | 29.2614 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7409 | 96.6568 | 98.8496 | 59.7558 | 29461 | 1019 | 60407 | 703 | 560 | 79.6586 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7409 | 96.6568 | 98.8496 | 59.7558 | 29461 | 1019 | 60407 | 703 | 560 | 79.6586 | |
| mlin-fermikit | INDEL | D1_5 | HG002compoundhet | homalt | 41.8824 | 90.7216 | 27.2257 | 80.6916 | 264 | 27 | 263 | 703 | 687 | 97.7240 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 11.0979 | 9.3988 | 13.5468 | 44.1924 | 111 | 1070 | 110 | 702 | 699 | 99.5726 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 22.0217 | 71.6216 | 13.0112 | 43.9194 | 106 | 42 | 105 | 702 | 699 | 99.5726 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 69.0860 | 69.8980 | 68.2927 | 72.8277 | 1507 | 649 | 1512 | 702 | 277 | 39.4587 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.4900 | 97.9500 | 77.4308 | 59.1746 | 2389 | 50 | 2405 | 701 | 19 | 2.7104 | |
| ckim-dragen | SNP | ti | map_l125_m2_e0 | * | 98.4121 | 99.1176 | 97.7165 | 74.4145 | 29991 | 267 | 29998 | 701 | 81 | 11.5549 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.1226 | 86.4620 | 96.3144 | 38.7578 | 4956 | 776 | 18319 | 701 | 658 | 93.8659 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e1 | * | 98.2162 | 98.7046 | 97.7326 | 76.3818 | 30173 | 396 | 30173 | 700 | 158 | 22.5714 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 63.6599 | 61.2245 | 66.2970 | 66.6238 | 1320 | 836 | 1375 | 699 | 438 | 62.6609 | |
| gduggal-bwafb | INDEL | I6_15 | HG002compoundhet | * | 80.9656 | 72.6869 | 91.3725 | 27.9246 | 6379 | 2397 | 7403 | 699 | 688 | 98.4263 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.4681 | 90.2214 | 92.7497 | 68.5930 | 9088 | 985 | 8942 | 699 | 645 | 92.2747 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e0 | * | 98.2029 | 98.6946 | 97.7160 | 76.3322 | 29863 | 395 | 29863 | 698 | 158 | 22.6361 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | * | 97.3122 | 96.7874 | 97.8426 | 54.8110 | 31664 | 1051 | 31656 | 698 | 573 | 82.0917 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.3657 | 89.9732 | 92.8019 | 79.8114 | 9063 | 1010 | 8999 | 698 | 633 | 90.6877 | |
| gduggal-snapfb | SNP | ti | map_l100_m0_e0 | * | 96.4920 | 96.2060 | 96.7797 | 70.0719 | 20945 | 826 | 20947 | 697 | 344 | 49.3544 | |
| ckim-gatk | INDEL | D1_5 | * | * | 99.4755 | 99.4262 | 99.5247 | 61.4945 | 145903 | 842 | 145958 | 697 | 326 | 46.7719 | |