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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7001-7050 / 86044 show all | |||||||||||||||
| ghariani-varprowl | SNP | tv | map_l250_m2_e1 | * | 94.5092 | 97.3937 | 91.7906 | 91.6664 | 2840 | 76 | 2840 | 254 | 35 | 13.7795 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4140 | 91.7105 | 97.2817 | 66.6928 | 9238 | 835 | 9090 | 254 | 209 | 82.2835 | |
| gduggal-snapvard | INDEL | D1_5 | map_l100_m0_e0 | het | 84.5932 | 97.4619 | 74.7264 | 88.6901 | 576 | 15 | 751 | 254 | 66 | 25.9843 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.4285 | 76.5337 | 94.1394 | 56.8627 | 4067 | 1247 | 4080 | 254 | 153 | 60.2362 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.7221 | 89.8362 | 97.9593 | 52.4760 | 9979 | 1129 | 12193 | 254 | 153 | 60.2362 | |
| gduggal-bwavard | SNP | tv | map_l250_m0_e0 | het | 79.9753 | 96.3287 | 68.3686 | 94.9097 | 551 | 21 | 549 | 254 | 3 | 1.1811 | |
| gduggal-bwavard | INDEL | * | map_l100_m0_e0 | het | 87.7147 | 97.5514 | 79.6800 | 90.8905 | 996 | 25 | 996 | 254 | 63 | 24.8031 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.2450 | 80.8166 | 97.1772 | 89.7454 | 8729 | 2072 | 8744 | 254 | 45 | 17.7165 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.9932 | 96.6906 | 97.2976 | 45.4909 | 9145 | 313 | 9145 | 254 | 242 | 95.2756 | |
| anovak-vg | INDEL | * | map_l150_m1_e0 | het | 70.8356 | 70.4094 | 71.2670 | 91.2380 | 602 | 253 | 630 | 254 | 71 | 27.9528 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.6266 | 99.2892 | 97.9729 | 65.4849 | 12432 | 89 | 12276 | 254 | 243 | 95.6693 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | het | 93.0974 | 94.0064 | 92.2058 | 56.4938 | 2933 | 187 | 2993 | 253 | 209 | 82.6087 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9367 | 98.4377 | 99.4408 | 75.9589 | 44988 | 714 | 44988 | 253 | 34 | 13.4387 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9367 | 98.4377 | 99.4408 | 75.9589 | 44988 | 714 | 44988 | 253 | 34 | 13.4387 | |
| egarrison-hhga | SNP | * | * | homalt | 99.9329 | 99.8872 | 99.9785 | 18.1960 | 1178830 | 1331 | 1178859 | 253 | 173 | 68.3794 | |
| dgrover-gatk | SNP | * | map_l150_m2_e1 | het | 98.9757 | 99.1897 | 98.7625 | 81.1801 | 20198 | 165 | 20192 | 253 | 50 | 19.7628 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.9526 | 84.9119 | 87.0190 | 57.3989 | 1784 | 317 | 1696 | 253 | 247 | 97.6285 | |
| ghariani-varprowl | SNP | ti | map_l250_m2_e1 | het | 95.1903 | 97.7872 | 92.7278 | 92.3245 | 3226 | 73 | 3226 | 253 | 51 | 20.1581 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 97.9611 | 99.4586 | 96.5079 | 63.7151 | 6981 | 38 | 6992 | 253 | 3 | 1.1858 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 76.0659 | 65.5275 | 90.6435 | 34.5437 | 2416 | 1271 | 2451 | 253 | 251 | 99.2095 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.5781 | 69.6835 | 98.3690 | 63.8094 | 15260 | 6639 | 15259 | 253 | 243 | 96.0474 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1080 | 34.9234 | 88.6547 | 58.7648 | 1984 | 3697 | 1977 | 253 | 213 | 84.1897 | |
| qzeng-custom | SNP | tv | map_l150_m2_e1 | het | 83.6864 | 74.4284 | 95.5746 | 89.7620 | 5469 | 1879 | 5464 | 253 | 208 | 82.2134 | |
| mlin-fermikit | SNP | ti | map_l250_m1_e0 | homalt | 53.4856 | 42.2526 | 72.8541 | 73.1257 | 679 | 928 | 679 | 253 | 229 | 90.5138 | |
| mlin-fermikit | SNP | tv | map_l250_m2_e0 | homalt | 50.5025 | 42.9029 | 61.3740 | 74.4739 | 402 | 535 | 402 | 253 | 237 | 93.6759 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 81.2972 | 84.9765 | 77.9232 | 58.9542 | 905 | 160 | 893 | 253 | 210 | 83.0040 | |
| ciseli-custom | SNP | ti | map_l250_m0_e0 | het | 64.5750 | 60.5996 | 69.1087 | 96.2053 | 566 | 368 | 566 | 253 | 6 | 2.3715 | |
| ckim-gatk | INDEL | I1_5 | * | homalt | 99.7125 | 99.8428 | 99.5825 | 55.2232 | 60333 | 95 | 60339 | 253 | 249 | 98.4190 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 79.1674 | 71.9397 | 88.0095 | 54.7793 | 1910 | 745 | 1857 | 253 | 201 | 79.4466 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6683 | 98.8300 | 92.7026 | 77.7557 | 3210 | 38 | 3214 | 253 | 21 | 8.3004 | |
| rpoplin-dv42 | SNP | * | HG002complexvar | * | 99.9179 | 99.8694 | 99.9664 | 18.9545 | 753396 | 985 | 753221 | 253 | 214 | 84.5850 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.5288 | 96.1960 | 94.8708 | 69.9124 | 4653 | 184 | 4661 | 252 | 157 | 62.3016 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.2033 | 94.2180 | 92.2102 | 45.7942 | 2982 | 183 | 2983 | 252 | 219 | 86.9048 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.9937 | 96.5215 | 93.5135 | 55.4063 | 3635 | 131 | 3633 | 252 | 82 | 32.5397 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.9937 | 96.5215 | 93.5135 | 55.4063 | 3635 | 131 | 3633 | 252 | 82 | 32.5397 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| anovak-vg | SNP | ti | map_siren | homalt | 94.0329 | 89.3343 | 99.2531 | 48.3941 | 33872 | 4044 | 33489 | 252 | 225 | 89.2857 | |
| anovak-vg | INDEL | * | map_l100_m0_e0 | het | 71.5575 | 68.7561 | 74.5968 | 89.0375 | 702 | 319 | 740 | 252 | 75 | 29.7619 | |
| gduggal-snapvard | INDEL | I16_PLUS | HG002complexvar | * | 1.7978 | 0.9167 | 46.1538 | 59.1623 | 12 | 1297 | 216 | 252 | 147 | 58.3333 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 81.2239 | 97.0100 | 69.8565 | 48.4904 | 584 | 18 | 584 | 252 | 251 | 99.6032 | |
| gduggal-bwafb | INDEL | D16_PLUS | * | het | 87.0129 | 80.9433 | 94.0664 | 49.5246 | 2557 | 602 | 3995 | 252 | 244 | 96.8254 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.8869 | 95.0176 | 94.7566 | 72.8903 | 4596 | 241 | 4554 | 252 | 104 | 41.2698 | |
| jpowers-varprowl | INDEL | * | segdup | * | 89.1593 | 88.3803 | 89.9522 | 94.2165 | 2259 | 297 | 2256 | 252 | 223 | 88.4921 | |
| jpowers-varprowl | INDEL | D6_15 | HG002compoundhet | homalt | 13.4561 | 79.1667 | 7.3529 | 47.3888 | 19 | 5 | 20 | 252 | 231 | 91.6667 | |
| jli-custom | INDEL | I6_15 | * | * | 97.9633 | 96.9786 | 98.9683 | 47.9648 | 24073 | 750 | 24077 | 251 | 222 | 88.4462 | |
| jmaeng-gatk | INDEL | I1_5 | * | homalt | 99.7149 | 99.8444 | 99.5857 | 55.4032 | 60334 | 94 | 60340 | 251 | 245 | 97.6096 | |
| ltrigg-rtg1 | INDEL | D1_5 | * | het | 99.2847 | 98.8627 | 99.7103 | 52.7629 | 86578 | 996 | 86378 | 251 | 52 | 20.7171 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.8820 | 96.0769 | 82.6897 | 71.8992 | 1200 | 49 | 1199 | 251 | 105 | 41.8327 | |