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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15601-15650 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | * | * | 99.4009 | 99.3458 | 99.4561 | 60.2776 | 342288 | 2254 | 342154 | 1871 | 1513 | 80.8658 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.5331 | 72.3481 | 93.3894 | 66.7128 | 22255 | 8506 | 22222 | 1573 | 1272 | 80.8646 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 30.1806 | 24.9718 | 38.1353 | 46.7618 | 663 | 1992 | 953 | 1546 | 1250 | 80.8538 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.0992 | 92.7022 | 83.9316 | 81.2018 | 470 | 37 | 491 | 94 | 76 | 80.8511 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | homalt | 89.8612 | 94.8097 | 85.4037 | 66.1053 | 274 | 15 | 275 | 47 | 38 | 80.8511 | |
| ckim-vqsr | INDEL | * | * | * | 99.2541 | 99.0614 | 99.4476 | 60.7768 | 341308 | 3234 | 341167 | 1895 | 1532 | 80.8443 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 54.2561 | 49.7820 | 59.6139 | 54.7156 | 1941 | 1958 | 3057 | 2071 | 1674 | 80.8305 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.9463 | 95.1598 | 98.8011 | 63.5083 | 6016 | 306 | 6016 | 73 | 59 | 80.8219 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.9463 | 95.1598 | 98.8011 | 63.5083 | 6016 | 306 | 6016 | 73 | 59 | 80.8219 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 22.2306 | 13.2826 | 68.1223 | 82.0392 | 157 | 1025 | 156 | 73 | 59 | 80.8219 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.6996 | 85.4251 | 85.9760 | 54.8462 | 633 | 108 | 1502 | 245 | 198 | 80.8163 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.9504 | 99.5147 | 90.7864 | 82.3867 | 3896 | 19 | 3902 | 396 | 320 | 80.8081 | |
| ndellapenna-hhga | INDEL | D1_5 | segdup | * | 97.6439 | 97.6428 | 97.6449 | 94.0680 | 1077 | 26 | 1078 | 26 | 21 | 80.7692 | |
| mlin-fermikit | INDEL | D1_5 | map_l150_m0_e0 | * | 60.5938 | 47.4048 | 83.9506 | 83.7513 | 137 | 152 | 136 | 26 | 21 | 80.7692 | |
| jpowers-varprowl | INDEL | I1_5 | map_siren | het | 93.3720 | 94.3486 | 92.4154 | 83.6731 | 1586 | 95 | 1584 | 130 | 105 | 80.7692 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.5586 | 96.7635 | 98.3668 | 86.6207 | 1465 | 49 | 1566 | 26 | 21 | 80.7692 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m0_e0 | het | 62.2449 | 63.5417 | 61.0000 | 91.6771 | 122 | 70 | 122 | 78 | 63 | 80.7692 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 28.1655 | 19.4631 | 50.9434 | 80.0000 | 29 | 120 | 27 | 26 | 21 | 80.7692 | |
| ckim-gatk | SNP | ti | HG002compoundhet | * | 99.4312 | 99.0159 | 99.8500 | 36.2044 | 17306 | 172 | 17306 | 26 | 21 | 80.7692 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.2898 | 93.2880 | 99.4913 | 26.4604 | 5073 | 365 | 5085 | 26 | 21 | 80.7692 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.4127 | 92.9323 | 89.9420 | 85.4816 | 618 | 47 | 465 | 52 | 42 | 80.7692 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.0122 | 93.7922 | 96.2644 | 75.4150 | 695 | 46 | 670 | 26 | 21 | 80.7692 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 76.6857 | 62.3443 | 99.5964 | 36.2241 | 6457 | 3900 | 6416 | 26 | 21 | 80.7692 | |
| eyeh-varpipe | INDEL | D1_5 | segdup | * | 97.2740 | 96.8268 | 97.7253 | 93.8542 | 1068 | 35 | 1117 | 26 | 21 | 80.7692 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002complexvar | het | 92.6198 | 92.8205 | 92.4200 | 56.3998 | 2896 | 224 | 2975 | 244 | 197 | 80.7377 | |
| gduggal-bwafb | INDEL | * | HG002compoundhet | het | 91.2904 | 85.5154 | 97.9020 | 36.8528 | 3501 | 593 | 30518 | 654 | 528 | 80.7339 | |
| anovak-vg | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.2998 | 97.7430 | 96.8606 | 48.6593 | 9874 | 228 | 10089 | 327 | 264 | 80.7339 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.2953 | 72.7965 | 97.3327 | 63.5457 | 10035 | 3750 | 10035 | 275 | 222 | 80.7273 | |
| ciseli-custom | INDEL | I1_5 | * | het | 91.4560 | 94.1106 | 88.9472 | 61.0454 | 74385 | 4655 | 74801 | 9295 | 7503 | 80.7208 | |
| gduggal-snapvard | INDEL | D6_15 | * | * | 65.0191 | 61.1567 | 69.4022 | 48.8917 | 15957 | 10135 | 16034 | 7069 | 5706 | 80.7186 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.9324 | 95.1886 | 98.7412 | 44.6522 | 3482 | 176 | 4471 | 57 | 46 | 80.7018 | |
| anovak-vg | INDEL | D1_5 | HG002complexvar | homalt | 92.9611 | 95.2727 | 90.7590 | 57.9711 | 10097 | 501 | 10224 | 1041 | 840 | 80.6916 | |
| ciseli-custom | SNP | tv | map_l125_m0_e0 | homalt | 85.0153 | 83.7461 | 86.3236 | 70.9690 | 1860 | 361 | 1862 | 295 | 238 | 80.6780 | |
| qzeng-custom | SNP | * | map_l100_m1_e0 | het | 87.7038 | 79.5123 | 97.7769 | 80.6669 | 36066 | 9293 | 35714 | 812 | 655 | 80.6650 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | het | 97.8863 | 98.0978 | 97.6758 | 52.4481 | 20370 | 395 | 20424 | 486 | 392 | 80.6584 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e0 | homalt | 97.6688 | 95.7005 | 99.7199 | 73.1870 | 11196 | 503 | 11035 | 31 | 25 | 80.6452 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | homalt | 97.6681 | 95.6963 | 99.7228 | 73.2280 | 11318 | 509 | 11153 | 31 | 25 | 80.6452 | |
| bgallagher-sentieon | INDEL | I1_5 | * | * | 99.4227 | 99.2586 | 99.5873 | 58.2134 | 149547 | 1117 | 149597 | 620 | 500 | 80.6452 | |
| bgallagher-sentieon | SNP | tv | * | homalt | 99.9838 | 99.9759 | 99.9918 | 19.9074 | 377032 | 91 | 377017 | 31 | 25 | 80.6452 | |
| gduggal-bwavard | SNP | * | map_l100_m2_e0 | homalt | 98.6138 | 97.3767 | 99.8826 | 62.7969 | 26801 | 722 | 26381 | 31 | 25 | 80.6452 | |
| gduggal-bwavard | SNP | * | map_l100_m2_e1 | homalt | 98.6017 | 97.3521 | 99.8837 | 62.7989 | 27060 | 736 | 26631 | 31 | 25 | 80.6452 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m2_e0 | homalt | 97.3783 | 98.5270 | 96.2560 | 85.4148 | 602 | 9 | 797 | 31 | 25 | 80.6452 | |
| anovak-vg | INDEL | I1_5 | HG002compoundhet | het | 51.6510 | 42.9412 | 64.7929 | 62.2549 | 365 | 485 | 4553 | 2474 | 1995 | 80.6386 | |
| ciseli-custom | SNP | * | map_l150_m2_e1 | homalt | 86.5594 | 84.7045 | 88.4973 | 73.1841 | 10018 | 1809 | 9994 | 1299 | 1047 | 80.6005 | |
| eyeh-varpipe | INDEL | C1_5 | HG002complexvar | * | 90.0749 | 85.7143 | 94.9030 | 78.7246 | 6 | 1 | 2495 | 134 | 108 | 80.5970 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 90.4890 | 90.6867 | 90.2922 | 79.9205 | 964 | 99 | 958 | 103 | 83 | 80.5825 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 49.1325 | 41.4437 | 60.3241 | 51.4691 | 3485 | 4924 | 6068 | 3991 | 3216 | 80.5813 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 40.2391 | 29.5082 | 63.2353 | 29.4815 | 36 | 86 | 301 | 175 | 141 | 80.5714 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | homalt | 86.5638 | 84.7166 | 88.4932 | 73.1740 | 9911 | 1788 | 9890 | 1286 | 1036 | 80.5599 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 44.1767 | 33.5366 | 64.7059 | 59.2000 | 55 | 109 | 66 | 36 | 29 | 80.5556 | |