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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21851-21900 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I1_5 | map_l125_m1_e0 | het | 96.3970 | 93.6214 | 99.3421 | 76.3363 | 455 | 31 | 453 | 3 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l150_m2_e1 | * | 97.8495 | 96.4010 | 99.3421 | 82.5287 | 750 | 28 | 755 | 5 | 1 | 20.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.6562 | 96.0265 | 99.3421 | 59.0296 | 145 | 6 | 151 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | * | segdup | het | 98.9505 | 98.5621 | 99.3421 | 95.0542 | 17068 | 249 | 17062 | 113 | 4 | 3.5398 | |
| jlack-gatk | INDEL | I1_5 | map_siren | homalt | 99.3823 | 99.4224 | 99.3421 | 78.6217 | 1205 | 7 | 1208 | 8 | 5 | 62.5000 | |
| hfeng-pmm2 | SNP | ti | map_l100_m1_e0 | het | 99.3403 | 99.3387 | 99.3419 | 67.8029 | 29744 | 198 | 29737 | 197 | 16 | 8.1218 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | homalt | 84.0320 | 72.8109 | 99.3418 | 88.4510 | 1979 | 739 | 1962 | 13 | 9 | 69.2308 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5813 | 99.8219 | 99.3418 | 57.3342 | 3924 | 7 | 3924 | 26 | 1 | 3.8462 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.0626 | 98.7852 | 99.3416 | 58.5661 | 3822 | 47 | 3772 | 25 | 22 | 88.0000 | |
| gduggal-snapfb | SNP | * | map_l250_m1_e0 | homalt | 95.4651 | 91.8798 | 99.3415 | 92.6863 | 2263 | 200 | 2263 | 15 | 9 | 60.0000 | |
| jpowers-varprowl | SNP | tv | map_l250_m2_e0 | homalt | 97.9437 | 96.5848 | 99.3414 | 90.7971 | 905 | 32 | 905 | 6 | 2 | 33.3333 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4723 | 99.6037 | 99.3412 | 88.4492 | 1508 | 6 | 1508 | 10 | 9 | 90.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.3169 | 89.7764 | 99.3411 | 33.3446 | 6182 | 704 | 1960 | 13 | 13 | 100.0000 | |
| dgrover-gatk | SNP | * | map_l125_m2_e1 | * | 99.3336 | 99.3263 | 99.3409 | 74.2508 | 46884 | 318 | 46878 | 311 | 69 | 22.1865 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3731 | 99.4054 | 99.3408 | 76.0979 | 47984 | 287 | 47771 | 317 | 259 | 81.7035 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.8622 | 85.4308 | 99.3408 | 88.0041 | 1507 | 257 | 1507 | 10 | 4 | 40.0000 | |
| ckim-isaac | INDEL | * | map_l125_m2_e1 | homalt | 73.5557 | 58.3979 | 99.3407 | 81.3295 | 452 | 322 | 452 | 3 | 1 | 33.3333 | |
| gduggal-bwavard | SNP | tv | map_l250_m2_e0 | homalt | 98.0530 | 96.7983 | 99.3407 | 88.0609 | 907 | 30 | 904 | 6 | 4 | 66.6667 | |
| asubramanian-gatk | INDEL | * | map_l150_m2_e1 | homalt | 95.3495 | 91.6667 | 99.3407 | 90.2129 | 451 | 41 | 452 | 3 | 1 | 33.3333 | |
| egarrison-hhga | INDEL | I1_5 | map_siren | homalt | 99.3814 | 99.4224 | 99.3405 | 78.4317 | 1205 | 7 | 1205 | 8 | 4 | 50.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m2_e0 | homalt | 99.2113 | 99.0826 | 99.3404 | 85.1285 | 756 | 7 | 753 | 5 | 3 | 60.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4059 | 99.4716 | 99.3404 | 88.6280 | 1506 | 8 | 1506 | 10 | 9 | 90.0000 | |
| hfeng-pmm2 | SNP | tv | segdup | het | 99.5467 | 99.7541 | 99.3402 | 91.9297 | 5274 | 13 | 5270 | 35 | 0 | 0.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9081 | 96.5168 | 99.3401 | 63.4667 | 15517 | 560 | 15655 | 104 | 87 | 83.6538 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.9081 | 96.5168 | 99.3401 | 63.4667 | 15517 | 560 | 15655 | 104 | 87 | 83.6538 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6082 | 99.8778 | 99.3401 | 60.0690 | 55563 | 68 | 55552 | 369 | 30 | 8.1301 | |
| rpoplin-dv42 | SNP | tv | map_l100_m2_e0 | * | 99.2885 | 99.2370 | 99.3401 | 66.0825 | 24842 | 191 | 24838 | 165 | 80 | 48.4848 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7118 | 98.0915 | 99.3400 | 56.1553 | 10896 | 212 | 10837 | 72 | 12 | 16.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3727 | 99.4055 | 99.3399 | 88.6347 | 1505 | 9 | 1505 | 10 | 9 | 90.0000 | |
| anovak-vg | SNP | * | map_l100_m2_e0 | homalt | 91.7943 | 85.3141 | 99.3397 | 61.4498 | 23481 | 4042 | 23170 | 154 | 133 | 86.3636 | |
| dgrover-gatk | INDEL | I1_5 | segdup | * | 99.2921 | 99.2446 | 99.3396 | 94.6513 | 1051 | 8 | 1053 | 7 | 2 | 28.5714 | |
| raldana-dualsentieon | INDEL | D1_5 | map_siren | het | 99.0760 | 98.8142 | 99.3392 | 78.2192 | 2250 | 27 | 2255 | 15 | 1 | 6.6667 | |
| anovak-vg | SNP | * | map_l100_m1_e0 | homalt | 91.6965 | 85.1461 | 99.3387 | 58.6113 | 22992 | 4011 | 22684 | 151 | 130 | 86.0927 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3478 | 99.3571 | 99.3386 | 42.1628 | 10663 | 69 | 10663 | 71 | 1 | 1.4085 | |
| gduggal-snapvard | SNP | ti | map_l150_m0_e0 | homalt | 96.4550 | 93.7342 | 99.3385 | 76.5596 | 2588 | 173 | 2553 | 17 | 13 | 76.4706 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002complexvar | * | 98.1740 | 97.0367 | 99.3383 | 57.2224 | 4650 | 142 | 4654 | 31 | 31 | 100.0000 | |
| raldana-dualsentieon | SNP | ti | map_siren | het | 99.3661 | 99.3941 | 99.3382 | 55.1273 | 62004 | 378 | 61995 | 413 | 8 | 1.9371 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.3986 | 97.4766 | 99.3382 | 61.3636 | 1352 | 35 | 1351 | 9 | 1 | 11.1111 | |
| jli-custom | SNP | * | map_l125_m2_e0 | het | 99.0801 | 98.8232 | 99.3382 | 70.5778 | 28973 | 345 | 28970 | 193 | 54 | 27.9793 | |
| ndellapenna-hhga | INDEL | I1_5 | map_siren | het | 98.8036 | 98.2748 | 99.3381 | 80.3824 | 1652 | 29 | 1651 | 11 | 1 | 9.0909 | |
| ndellapenna-hhga | SNP | tv | map_l250_m1_e0 | * | 97.8332 | 96.3733 | 99.3380 | 86.1787 | 2551 | 96 | 2551 | 17 | 10 | 58.8235 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.5027 | 97.6813 | 99.3380 | 83.9369 | 2654 | 63 | 2551 | 17 | 1 | 5.8824 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 91.6942 | 85.1429 | 99.3377 | 63.8756 | 149 | 26 | 150 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | HG002complexvar | hetalt | 96.3423 | 93.5223 | 99.3377 | 47.4478 | 231 | 16 | 450 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | segdup | * | 99.1492 | 98.9613 | 99.3377 | 93.8436 | 1048 | 11 | 1050 | 7 | 3 | 42.8571 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 92.6924 | 86.8805 | 99.3377 | 58.4022 | 298 | 45 | 300 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e1 | homalt | 96.3001 | 93.4426 | 99.3377 | 85.6787 | 1197 | 84 | 1200 | 8 | 3 | 37.5000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.2100 | 97.1081 | 99.3372 | 24.1239 | 4634 | 138 | 4646 | 31 | 30 | 96.7742 | |
| rpoplin-dv42 | INDEL | * | * | hetalt | 95.6899 | 92.3010 | 99.3372 | 57.2847 | 23294 | 1943 | 23381 | 156 | 151 | 96.7949 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3508 | 99.3647 | 99.3369 | 68.1260 | 3128 | 20 | 3146 | 21 | 3 | 14.2857 | |