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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69451-69500 / 86044 show all | |||||||||||||||
| qzeng-custom | SNP | * | segdup | homalt | 99.2653 | 99.1250 | 99.4061 | 87.8458 | 10649 | 94 | 10544 | 63 | 57 | 90.4762 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.0231 | 94.1723 | 93.8743 | 38.5973 | 1519 | 94 | 8260 | 539 | 525 | 97.4026 | |
| jpowers-varprowl | SNP | tv | map_l125_m2_e1 | homalt | 98.9247 | 98.4524 | 99.4016 | 73.5688 | 5980 | 94 | 5980 | 36 | 25 | 69.4444 | |
| jli-custom | SNP | * | map_l250_m0_e0 | * | 97.2831 | 95.5972 | 99.0296 | 90.2998 | 2041 | 94 | 2041 | 20 | 12 | 60.0000 | |
| jli-custom | SNP | ti | map_siren | homalt | 99.8561 | 99.7521 | 99.9604 | 48.6440 | 37822 | 94 | 37819 | 15 | 15 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.0868 | 99.0968 | 99.0767 | 50.8276 | 10313 | 94 | 10302 | 96 | 89 | 92.7083 | |
| jmaeng-gatk | INDEL | D6_15 | * | het | 98.5809 | 99.1891 | 97.9801 | 63.8389 | 11498 | 94 | 11448 | 236 | 191 | 80.9322 | |
| jmaeng-gatk | INDEL | I1_5 | * | homalt | 99.7149 | 99.8444 | 99.5857 | 55.4032 | 60334 | 94 | 60340 | 251 | 245 | 97.6096 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | homalt | 98.7666 | 98.4933 | 99.0414 | 43.6510 | 6145 | 94 | 6096 | 59 | 52 | 88.1356 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e1 | het | 92.8294 | 93.3239 | 92.3401 | 89.9662 | 1314 | 94 | 1314 | 109 | 76 | 69.7248 | |
| jpowers-varprowl | INDEL | * | segdup | homalt | 93.9252 | 90.2083 | 97.9615 | 91.6422 | 866 | 94 | 865 | 18 | 17 | 94.4444 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9501 | 99.4036 | 98.5008 | 62.9678 | 15666 | 94 | 15506 | 236 | 204 | 86.4407 | |
| ciseli-custom | INDEL | I6_15 | map_l100_m2_e0 | * | 29.5302 | 18.9655 | 66.6667 | 89.9083 | 22 | 94 | 22 | 11 | 10 | 90.9091 | |
| ciseli-custom | INDEL | I6_15 | map_l100_m2_e1 | * | 29.5302 | 18.9655 | 66.6667 | 90.0000 | 22 | 94 | 22 | 11 | 10 | 90.9091 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 92.1339 | 0.0000 | 0.0000 | 1101 | 94 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | map_l125_m2_e1 | * | 96.8910 | 95.7753 | 98.0329 | 87.0344 | 2131 | 94 | 2143 | 43 | 9 | 20.9302 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 61.5270 | 78.8288 | 50.4532 | 56.2459 | 350 | 94 | 334 | 328 | 326 | 99.3902 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 21.6364 | 12.9630 | 65.3846 | 59.3750 | 14 | 94 | 17 | 9 | 9 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.9308 | 89.1078 | 90.7692 | 60.4401 | 769 | 94 | 767 | 78 | 76 | 97.4359 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.4657 | 93.1034 | 95.8683 | 72.1692 | 1269 | 94 | 1369 | 59 | 47 | 79.6610 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.0456 | 96.0304 | 83.0080 | 88.0462 | 2274 | 94 | 2296 | 470 | 74 | 15.7447 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.4259 | 97.9953 | 96.8630 | 51.4454 | 4595 | 94 | 4539 | 147 | 42 | 28.5714 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 88.8215 | 82.4299 | 96.2877 | 75.1298 | 441 | 94 | 415 | 16 | 14 | 87.5000 | |
| gduggal-bwavard | INDEL | * | map_l100_m2_e1 | homalt | 95.8810 | 92.6620 | 99.3317 | 77.1434 | 1187 | 94 | 1189 | 8 | 5 | 62.5000 | |
| 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 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9876 | 99.1538 | 98.8219 | 62.9494 | 11014 | 94 | 10989 | 131 | 41 | 31.2977 | |
| jlack-gatk | SNP | ti | map_l250_m1_e0 | * | 94.0942 | 97.9472 | 90.5329 | 92.4177 | 4485 | 94 | 4485 | 469 | 43 | 9.1684 | |
| hfeng-pmm1 | INDEL | * | map_siren | het | 98.4945 | 97.9148 | 99.0811 | 80.4769 | 4414 | 94 | 4421 | 41 | 3 | 7.3171 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2060 | 98.6004 | 99.8192 | 50.8699 | 6622 | 94 | 6624 | 12 | 3 | 25.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.8947 | 98.7270 | 95.1293 | 53.9091 | 7290 | 94 | 7285 | 373 | 354 | 94.9062 | |
| rpoplin-dv42 | INDEL | D6_15 | * | homalt | 99.1567 | 98.5141 | 99.8078 | 51.4461 | 6232 | 94 | 6233 | 12 | 7 | 58.3333 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.5554 | 99.5199 | 99.5910 | 69.5435 | 19485 | 94 | 19481 | 80 | 32 | 40.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.5554 | 99.5199 | 99.5910 | 69.5435 | 19485 | 94 | 19481 | 80 | 32 | 40.0000 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e1 | * | 97.9158 | 97.4973 | 98.3378 | 98.2252 | 3662 | 94 | 3668 | 62 | 29 | 46.7742 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 28.7879 | 0.0000 | 0.0000 | 38 | 94 | 0 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | het | 83.5823 | 96.6936 | 73.6022 | 87.1311 | 2749 | 94 | 2738 | 982 | 41 | 4.1752 | |
| ghariani-varprowl | INDEL | * | map_l100_m0_e0 | * | 90.4000 | 93.9859 | 87.0777 | 93.2660 | 1469 | 94 | 1469 | 218 | 66 | 30.2752 | |
| ghariani-varprowl | INDEL | * | segdup | homalt | 93.7217 | 90.2083 | 97.5197 | 91.8211 | 866 | 94 | 865 | 22 | 17 | 77.2727 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 55.0165 | 87.3144 | 40.1609 | 56.7914 | 647 | 94 | 649 | 967 | 945 | 97.7249 | |
| gduggal-snapfb | SNP | * | HG002compoundhet | homalt | 96.1466 | 99.1282 | 93.3392 | 44.8696 | 10688 | 94 | 10692 | 763 | 275 | 36.0419 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m2_e0 | * | 76.6354 | 64.3939 | 94.6237 | 81.8182 | 170 | 94 | 176 | 10 | 9 | 90.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 82.7682 | 83.3333 | 82.2107 | 69.9221 | 470 | 94 | 476 | 103 | 33 | 32.0388 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.8708 | 55.0239 | 56.7442 | 69.7183 | 115 | 94 | 122 | 93 | 53 | 56.9892 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 59.0564 | 88.9542 | 44.2005 | 85.0316 | 757 | 94 | 785 | 991 | 11 | 1.1100 | |
| ghariani-varprowl | SNP | tv | map_l125_m1_e0 | homalt | 98.8683 | 98.3959 | 99.3453 | 69.2128 | 5766 | 94 | 5766 | 38 | 24 | 63.1579 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 45.3517 | 52.2843 | 40.0424 | 58.1189 | 103 | 94 | 189 | 283 | 245 | 86.5724 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m1_e0 | het | 83.5667 | 80.4979 | 86.8787 | 94.5219 | 388 | 94 | 437 | 66 | 17 | 25.7576 | |
| gduggal-snapplat | INDEL | D6_15 | map_l100_m2_e1 | het | 43.1266 | 30.3704 | 74.3590 | 93.8967 | 41 | 94 | 29 | 10 | 1 | 10.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m1_e0 | homalt | 87.6307 | 81.8533 | 94.2857 | 87.4897 | 424 | 94 | 429 | 26 | 1 | 3.8462 | |
| anovak-vg | INDEL | * | map_l250_m1_e0 | * | 66.8127 | 69.1803 | 64.6018 | 96.2450 | 211 | 94 | 219 | 120 | 61 | 50.8333 | |