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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
47151-47200 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | * | HG002compoundhet | homalt | 47.4306 | 99.5627 | 31.1304 | 79.5488 | 683 | 3 | 683 | 1511 | 1501 | 99.3382 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3618 | 90.6883 | 96.1977 | 79.5490 | 224 | 23 | 253 | 10 | 6 | 60.0000 | |
| jmaeng-gatk | INDEL | * | HG002compoundhet | het | 92.6044 | 97.8749 | 87.8724 | 79.5506 | 4007 | 87 | 3775 | 521 | 513 | 98.4645 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 75.4098 | 95.8333 | 62.1622 | 79.5580 | 23 | 1 | 23 | 14 | 14 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.4391 | 88.9344 | 87.9493 | 79.5592 | 434 | 54 | 416 | 57 | 55 | 96.4912 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.3706 | 95.4839 | 99.3333 | 79.5640 | 148 | 7 | 149 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | * | func_cds | * | 95.4669 | 93.9326 | 97.0522 | 79.5644 | 418 | 27 | 428 | 13 | 11 | 84.6154 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.6923 | 95.5844 | 97.8261 | 79.5669 | 368 | 17 | 360 | 8 | 7 | 87.5000 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | het | 11.7249 | 76.4706 | 6.3492 | 79.5676 | 13 | 4 | 12 | 177 | 2 | 1.1299 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | * | 89.5170 | 82.2096 | 98.2503 | 79.5686 | 61441 | 13296 | 61430 | 1094 | 86 | 7.8611 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.6328 | 98.1185 | 99.1525 | 79.5691 | 1043 | 20 | 1053 | 9 | 5 | 55.5556 | |
| astatham-gatk | SNP | * | map_l150_m2_e0 | hetalt | 97.4359 | 95.0000 | 100.0000 | 79.5699 | 19 | 1 | 19 | 0 | 0 | ||
| astatham-gatk | SNP | * | map_l150_m2_e1 | hetalt | 97.4359 | 95.0000 | 100.0000 | 79.5699 | 19 | 1 | 19 | 0 | 0 | ||
| astatham-gatk | SNP | tv | map_l150_m2_e0 | hetalt | 97.4359 | 95.0000 | 100.0000 | 79.5699 | 19 | 1 | 19 | 0 | 0 | ||
| astatham-gatk | SNP | tv | map_l150_m2_e1 | hetalt | 97.4359 | 95.0000 | 100.0000 | 79.5699 | 19 | 1 | 19 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.3899 | 96.1290 | 98.6842 | 79.5699 | 149 | 6 | 150 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.8264 | 99.4530 | 88.8023 | 79.5703 | 909 | 5 | 912 | 115 | 1 | 0.8696 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.4955 | 96.8668 | 94.1624 | 79.5749 | 371 | 12 | 371 | 23 | 18 | 78.2609 | |
| qzeng-custom | INDEL | C16_PLUS | map_l100_m2_e0 | * | 0.0000 | 0.0000 | 79.5775 | 0 | 0 | 0 | 29 | 0 | 0.0000 | ||
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3974 | 99.2449 | 99.5503 | 79.5805 | 4206 | 32 | 4206 | 19 | 5 | 26.3158 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.8553 | 95.0617 | 98.7179 | 79.5812 | 77 | 4 | 77 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 95.8314 | 95.7447 | 95.9184 | 79.5833 | 45 | 2 | 47 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8428 | 99.7906 | 99.8952 | 79.5848 | 953 | 2 | 953 | 1 | 0 | 0.0000 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 44.0468 | 83.2421 | 29.9463 | 79.5867 | 760 | 153 | 781 | 1827 | 29 | 1.5873 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | * | 89.4294 | 82.0710 | 98.2373 | 79.5869 | 60703 | 13261 | 60692 | 1089 | 86 | 7.8972 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.1378 | 93.1174 | 97.2477 | 79.5880 | 230 | 17 | 212 | 6 | 4 | 66.6667 | |
| anovak-vg | INDEL | * | map_l100_m1_e0 | homalt | 76.5861 | 87.2046 | 68.2728 | 79.5887 | 1070 | 157 | 1091 | 507 | 474 | 93.4911 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e1 | het | 98.3690 | 98.4710 | 98.2671 | 79.5893 | 12816 | 199 | 12816 | 226 | 64 | 28.3186 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e0 | het | 99.0233 | 99.1926 | 98.8546 | 79.5912 | 12777 | 104 | 12773 | 148 | 13 | 8.7838 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m2_e1 | homalt | 90.7434 | 84.0323 | 98.6196 | 79.5931 | 521 | 99 | 643 | 9 | 9 | 100.0000 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e0 | het | 98.9416 | 99.1556 | 98.7286 | 79.5932 | 19963 | 170 | 19957 | 257 | 23 | 8.9494 | |
| hfeng-pmm2 | SNP | tv | map_l150_m2_e0 | het | 98.7968 | 99.0899 | 98.5054 | 79.5966 | 7186 | 66 | 7184 | 109 | 10 | 9.1743 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m2_e1 | homalt | 82.8272 | 72.2222 | 97.0827 | 79.5966 | 390 | 150 | 599 | 18 | 3 | 16.6667 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 78.2077 | 80.0368 | 76.4603 | 79.5968 | 1740 | 434 | 1741 | 536 | 6 | 1.1194 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 58.9260 | 45.7207 | 82.8571 | 79.6003 | 609 | 723 | 609 | 126 | 21 | 16.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | map_siren | * | 99.1319 | 98.7354 | 99.5316 | 79.6028 | 2967 | 38 | 2975 | 14 | 4 | 28.5714 | |
| hfeng-pmm2 | SNP | tv | map_l150_m2_e1 | het | 98.8125 | 99.1018 | 98.5248 | 79.6036 | 7282 | 66 | 7280 | 109 | 10 | 9.1743 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.7610 | 94.3089 | 80.3318 | 79.6037 | 348 | 21 | 339 | 83 | 46 | 55.4217 | |
| ckim-gatk | INDEL | * | HG002compoundhet | het | 93.4586 | 98.5589 | 88.8602 | 79.6039 | 4035 | 59 | 3789 | 475 | 465 | 97.8947 | |
| gduggal-bwafb | SNP | * | map_l150_m2_e0 | het | 98.2282 | 98.4453 | 98.0121 | 79.6044 | 19820 | 313 | 19820 | 402 | 96 | 23.8806 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.3517 | 93.1174 | 97.6959 | 79.6053 | 230 | 17 | 212 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.4006 | 94.8267 | 92.0168 | 79.6069 | 3831 | 209 | 3723 | 323 | 189 | 58.5139 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 84.3374 | 74.7117 | 96.8102 | 79.6075 | 3628 | 1228 | 3642 | 120 | 34 | 28.3333 | |
| ltrigg-rtg1 | INDEL | D6_15 | map_siren | * | 97.5076 | 96.4637 | 98.5743 | 79.6096 | 491 | 18 | 484 | 7 | 1 | 14.2857 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7995 | 99.6662 | 99.9331 | 79.6097 | 1493 | 5 | 1493 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.0864 | 98.7941 | 97.3887 | 79.6107 | 6800 | 83 | 6825 | 183 | 3 | 1.6393 | |
| jli-custom | INDEL | I6_15 | map_l100_m1_e0 | hetalt | 97.6744 | 95.4545 | 100.0000 | 79.6117 | 21 | 1 | 21 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.4841 | 98.2647 | 98.7045 | 79.6128 | 92810 | 1639 | 92797 | 1218 | 1144 | 93.9245 | |
| rpoplin-dv42 | INDEL | * | map_siren | homalt | 99.1894 | 99.0584 | 99.3208 | 79.6138 | 2630 | 25 | 2632 | 18 | 11 | 61.1111 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m2_e0 | het | 96.2239 | 93.3861 | 99.2395 | 79.6156 | 1299 | 92 | 1305 | 10 | 0 | 0.0000 | |