PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74451-74500 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I16_PLUS | HG002compoundhet | het | 8.3916 | 12.7660 | 6.2500 | 77.0883 | 6 | 41 | 6 | 90 | 75 | 83.3333 | |
| ciseli-custom | SNP | * | func_cds | homalt | 99.2844 | 99.8567 | 98.7187 | 22.2148 | 6969 | 10 | 6934 | 90 | 38 | 42.2222 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 94.9226 | 99.8834 | 90.4311 | 55.1415 | 857 | 1 | 860 | 91 | 16 | 17.5824 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.5003 | 98.6256 | 94.4647 | 86.9451 | 1794 | 25 | 1553 | 91 | 38 | 41.7582 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.5003 | 98.6256 | 94.4647 | 86.9451 | 1794 | 25 | 1553 | 91 | 38 | 41.7582 | |
| ckim-isaac | INDEL | * | map_siren | het | 87.7323 | 79.7249 | 97.5278 | 80.3155 | 3594 | 914 | 3590 | 91 | 35 | 38.4615 | |
| cchapple-custom | INDEL | * | map_l100_m0_e0 | * | 95.2252 | 96.0972 | 94.3688 | 85.7659 | 1502 | 61 | 1525 | 91 | 22 | 24.1758 | |
| cchapple-custom | INDEL | C1_5 | * | het | 91.7367 | 88.8889 | 94.7731 | 92.2595 | 8 | 1 | 1650 | 91 | 24 | 26.3736 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.3154 | 98.5106 | 96.1490 | 77.8952 | 2381 | 36 | 2272 | 91 | 31 | 34.0659 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2808 | 98.8889 | 99.6759 | 57.1851 | 27946 | 314 | 27984 | 91 | 76 | 83.5165 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 64.6064 | 50.2642 | 90.4008 | 85.4064 | 856 | 847 | 857 | 91 | 11 | 12.0879 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | homalt | 96.4038 | 94.2115 | 98.7006 | 34.6979 | 6966 | 428 | 6912 | 91 | 82 | 90.1099 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.1269 | 99.7642 | 96.5426 | 62.1131 | 2538 | 6 | 2541 | 91 | 11 | 12.0879 | |
| jli-custom | SNP | ti | map_l150_m2_e1 | het | 98.9202 | 98.5478 | 99.2954 | 74.8618 | 12826 | 189 | 12824 | 91 | 30 | 32.9670 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e1 | het | 94.4493 | 95.8991 | 93.0428 | 86.2663 | 1216 | 52 | 1217 | 91 | 62 | 68.1319 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.7392 | 94.6612 | 83.5145 | 64.2718 | 461 | 26 | 461 | 91 | 89 | 97.8022 | |
| jpowers-varprowl | SNP | ti | map_l250_m0_e0 | het | 90.9574 | 91.5418 | 90.3805 | 95.3348 | 855 | 79 | 855 | 91 | 17 | 18.6813 | |
| ltrigg-rtg1 | SNP | ti | map_l100_m1_e0 | * | 99.3155 | 98.8275 | 99.8083 | 56.5736 | 47369 | 562 | 47371 | 91 | 27 | 29.6703 | |
| ghariani-varprowl | SNP | * | map_l100_m1_e0 | homalt | 99.3219 | 98.9853 | 99.6607 | 61.9023 | 26729 | 274 | 26729 | 91 | 64 | 70.3297 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.6463 | 99.5904 | 97.7199 | 44.7612 | 3890 | 16 | 3900 | 91 | 9 | 9.8901 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 86.9295 | 80.9834 | 93.8179 | 77.6360 | 1367 | 321 | 1381 | 91 | 39 | 42.8571 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 79.6041 | 74.3750 | 85.6240 | 66.7717 | 119 | 41 | 542 | 91 | 45 | 49.4505 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 71.9478 | 78.1377 | 66.6667 | 74.2938 | 193 | 54 | 182 | 91 | 90 | 98.9011 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.5975 | 97.2222 | 88.3929 | 44.7887 | 210 | 6 | 693 | 91 | 41 | 45.0549 | |
| qzeng-custom | SNP | * | map_l125_m1_e0 | homalt | 83.2331 | 71.6711 | 99.2430 | 64.3421 | 12116 | 4789 | 11930 | 91 | 90 | 98.9011 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.0557 | 90.2945 | 95.9912 | 59.3990 | 2177 | 234 | 2179 | 91 | 83 | 91.2088 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 89.6161 | 97.7492 | 82.7324 | 63.1469 | 304 | 7 | 436 | 91 | 90 | 98.9011 | |
| bgallagher-sentieon | SNP | tv | map_l150_m0_e0 | * | 98.4884 | 99.1375 | 97.8477 | 81.2755 | 4138 | 36 | 4137 | 91 | 10 | 10.9890 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 86.3345 | 95.2646 | 78.9352 | 39.3258 | 342 | 17 | 341 | 91 | 89 | 97.8022 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.0900 | 99.5359 | 98.6480 | 56.8443 | 6648 | 31 | 6640 | 91 | 88 | 96.7033 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.9055 | 69.1535 | 84.1187 | 50.6034 | 482 | 215 | 482 | 91 | 88 | 96.7033 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | het | 98.1499 | 98.0554 | 98.2446 | 88.1117 | 5093 | 101 | 5093 | 91 | 56 | 61.5385 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.5845 | 92.0383 | 99.4149 | 38.4055 | 15375 | 1330 | 15461 | 91 | 90 | 98.9011 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.5845 | 92.0383 | 99.4149 | 38.4055 | 15375 | 1330 | 15461 | 91 | 90 | 98.9011 | |
| egarrison-hhga | INDEL | * | HG002complexvar | hetalt | 86.1120 | 77.4804 | 96.9079 | 71.2204 | 2866 | 833 | 2852 | 91 | 84 | 92.3077 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4966 | 99.3171 | 99.6769 | 61.8156 | 28067 | 193 | 28070 | 91 | 68 | 74.7253 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6094 | 95.5357 | 95.6831 | 73.2283 | 2033 | 95 | 2017 | 91 | 76 | 83.5165 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.0824 | 99.5209 | 98.6478 | 57.7394 | 6647 | 32 | 6639 | 91 | 89 | 97.8022 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.0250 | 99.3414 | 96.7430 | 63.3526 | 2715 | 18 | 2703 | 91 | 87 | 95.6044 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2848 | 99.4427 | 99.1274 | 50.6623 | 10349 | 58 | 10338 | 91 | 83 | 91.2088 | |
| hfeng-pmm1 | SNP | ti | map_l125_m2_e1 | * | 99.4622 | 99.2247 | 99.7008 | 70.5014 | 30332 | 237 | 30328 | 91 | 25 | 27.4725 | |
| hfeng-pmm3 | SNP | ti | map_l100_m1_e0 | het | 99.5602 | 99.4256 | 99.6952 | 64.3351 | 29770 | 172 | 29763 | 91 | 9 | 9.8901 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 89.3082 | 97.4828 | 82.3985 | 47.2449 | 426 | 11 | 426 | 91 | 91 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.4410 | 99.4368 | 95.5239 | 41.0041 | 1942 | 11 | 1942 | 91 | 91 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | segdup | * | 99.6754 | 99.8157 | 99.5355 | 89.6871 | 19501 | 36 | 19499 | 91 | 9 | 9.8901 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4896 | 97.3839 | 99.6207 | 39.3186 | 23898 | 642 | 23900 | 91 | 86 | 94.5055 | |
| jlack-gatk | INDEL | I1_5 | segdup | * | 95.3193 | 98.8669 | 92.0175 | 95.4565 | 1047 | 12 | 1049 | 91 | 3 | 3.2967 | |
| hfeng-pmm1 | SNP | * | map_l125_m0_e0 | het | 98.9783 | 98.6892 | 99.2691 | 75.8999 | 12498 | 166 | 12495 | 92 | 24 | 26.0870 | |
| hfeng-pmm1 | SNP | * | map_l150_m0_e0 | * | 99.0843 | 98.9362 | 99.2329 | 79.6567 | 11904 | 128 | 11901 | 92 | 18 | 19.5652 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | homalt | 99.7542 | 99.8483 | 99.6603 | 56.1296 | 26986 | 41 | 26994 | 92 | 86 | 93.4783 | |