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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1551-1600 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 63.4268 | 61.9457 | 64.9805 | 71.6420 | 3171 | 1948 | 4342 | 2340 | 1455 | 62.1795 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 82.7904 | 78.6275 | 87.4187 | 53.2630 | 15617 | 4245 | 16259 | 2340 | 997 | 42.6068 | |
| gduggal-snapvard | SNP | * | map_l150_m0_e0 | * | 88.5661 | 95.0964 | 82.8750 | 85.4707 | 11442 | 590 | 11300 | 2335 | 147 | 6.2955 | |
| bgallagher-sentieon | INDEL | * | * | * | 99.2678 | 99.2143 | 99.3213 | 59.6036 | 341835 | 2707 | 341703 | 2335 | 1924 | 82.3983 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 91.4953 | 90.7025 | 92.3021 | 74.5517 | 27901 | 2860 | 27890 | 2326 | 2006 | 86.2425 | |
| gduggal-bwavard | SNP | ti | HG002complexvar | * | 98.2991 | 97.1039 | 99.5241 | 18.2603 | 493712 | 14725 | 485576 | 2322 | 1599 | 68.8630 | |
| gduggal-bwavard | INDEL | I16_PLUS | * | * | 58.4101 | 56.2490 | 60.7439 | 65.3100 | 3587 | 2790 | 3593 | 2322 | 1708 | 73.5573 | |
| ckim-isaac | INDEL | * | HG002complexvar | het | 92.2376 | 90.0654 | 94.5171 | 48.6355 | 41621 | 4591 | 40028 | 2322 | 1017 | 43.7984 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | het | 97.0873 | 95.7892 | 98.4210 | 25.5027 | 144384 | 6347 | 144674 | 2321 | 283 | 12.1930 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e1 | * | 92.6900 | 96.1203 | 89.4961 | 82.4891 | 19919 | 804 | 19733 | 2316 | 191 | 8.2470 | |
| gduggal-snapvard | SNP | * | map_l150_m0_e0 | het | 85.0213 | 95.7305 | 76.4670 | 87.2666 | 7601 | 339 | 7519 | 2314 | 131 | 5.6612 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.4077 | 96.8613 | 95.9584 | 55.0491 | 27373 | 887 | 54846 | 2310 | 1901 | 82.2944 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e0 | * | 92.6480 | 96.1047 | 89.4313 | 82.4164 | 19713 | 799 | 19530 | 2308 | 189 | 8.1889 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.0742 | 97.1085 | 74.1248 | 53.6075 | 6549 | 195 | 6606 | 2306 | 39 | 1.6912 | |
| gduggal-snapfb | INDEL | D1_5 | HG002compoundhet | * | 80.1461 | 78.4226 | 81.9472 | 64.9485 | 9595 | 2640 | 10454 | 2303 | 1568 | 68.0851 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 74.2102 | 70.4505 | 78.3938 | 47.6036 | 8366 | 3509 | 8356 | 2303 | 2257 | 98.0026 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.7140 | 88.5981 | 95.0570 | 53.8425 | 38394 | 4941 | 44230 | 2300 | 2147 | 93.3478 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | * | 92.4318 | 96.0278 | 89.0953 | 81.2252 | 18929 | 783 | 18751 | 2295 | 187 | 8.1482 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e1 | het | 90.0889 | 96.5271 | 84.4559 | 85.0397 | 12563 | 452 | 12464 | 2294 | 173 | 7.5414 | |
| gduggal-snapplat | SNP | tv | HG002compoundhet | het | 71.6435 | 82.9018 | 63.0774 | 69.0248 | 3874 | 799 | 3919 | 2294 | 156 | 6.8004 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 86.9581 | 84.9537 | 89.0595 | 73.1224 | 18604 | 3295 | 18674 | 2294 | 1762 | 76.8091 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 68.3237 | 77.6667 | 60.9872 | 71.9758 | 2330 | 670 | 3583 | 2292 | 1410 | 61.5183 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.1651 | 84.7285 | 77.8894 | 53.1421 | 8067 | 1454 | 8067 | 2290 | 2086 | 91.0917 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 76.0161 | 83.1560 | 70.0052 | 27.1233 | 469 | 95 | 5340 | 2288 | 2284 | 99.8252 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e0 | het | 90.0316 | 96.5142 | 84.3650 | 84.9671 | 12432 | 449 | 12335 | 2286 | 171 | 7.4803 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.7836 | 98.6301 | 74.3463 | 50.8169 | 6624 | 92 | 6625 | 2286 | 2211 | 96.7192 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 87.7988 | 86.5556 | 89.0781 | 44.8149 | 17827 | 2769 | 18620 | 2283 | 1417 | 62.0675 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 68.7702 | 67.0305 | 70.6027 | 63.8943 | 3808 | 1873 | 5471 | 2278 | 1700 | 74.6269 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.2180 | 98.6853 | 93.8711 | 58.0279 | 16213 | 216 | 34875 | 2277 | 1868 | 82.0378 | |
| gduggal-bwavard | INDEL | I16_PLUS | * | het | 66.4433 | 91.0228 | 52.3161 | 67.5288 | 2474 | 244 | 2496 | 2275 | 1694 | 74.4615 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | het | 89.7218 | 96.4268 | 83.8886 | 83.9806 | 11928 | 442 | 11835 | 2273 | 169 | 7.4351 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 74.5876 | 79.0062 | 70.6370 | 92.2018 | 5438 | 1445 | 5456 | 2268 | 88 | 3.8801 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.4933 | 92.7475 | 86.4597 | 53.2254 | 14617 | 1143 | 14482 | 2268 | 2204 | 97.1781 | |
| mlin-fermikit | SNP | * | map_l150_m1_e0 | * | 56.5558 | 42.3405 | 85.1406 | 61.3631 | 12960 | 17649 | 12955 | 2261 | 1991 | 88.0584 | |
| jlack-gatk | SNP | tv | map_siren | * | 97.3060 | 99.4187 | 95.2813 | 67.8334 | 45663 | 267 | 45655 | 2261 | 122 | 5.3958 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 89.9321 | 98.7700 | 82.5458 | 58.4226 | 10600 | 132 | 10674 | 2257 | 114 | 5.0510 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.6106 | 86.8839 | 88.3495 | 88.3802 | 17011 | 2568 | 17070 | 2251 | 184 | 8.1741 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.6106 | 86.8839 | 88.3495 | 88.3802 | 17011 | 2568 | 17070 | 2251 | 184 | 8.1741 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 81.2064 | 88.9071 | 74.7333 | 41.7707 | 5971 | 745 | 6655 | 2250 | 1626 | 72.2667 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 37.3916 | 32.4297 | 44.1462 | 77.4584 | 1292 | 2692 | 1776 | 2247 | 890 | 39.6084 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.8694 | 82.8315 | 89.1386 | 45.6102 | 18430 | 3820 | 18400 | 2242 | 2180 | 97.2346 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 45.1124 | 44.6159 | 45.6200 | 29.5676 | 1330 | 1651 | 1880 | 2241 | 2138 | 95.4038 | |
| jlack-gatk | SNP | tv | map_siren | het | 95.9855 | 99.5106 | 92.7015 | 72.5215 | 28469 | 140 | 28464 | 2241 | 108 | 4.8193 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 55.0228 | 69.6517 | 45.4722 | 29.4037 | 420 | 183 | 1868 | 2240 | 2137 | 95.4018 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 78.2056 | 76.4379 | 80.0570 | 49.9353 | 9077 | 2798 | 8988 | 2239 | 1967 | 87.8517 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.3755 | 92.9518 | 86.0642 | 79.3543 | 13544 | 1027 | 13809 | 2236 | 557 | 24.9106 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.3755 | 92.9518 | 86.0642 | 79.3543 | 13544 | 1027 | 13809 | 2236 | 557 | 24.9106 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.9665 | 98.6599 | 74.6109 | 52.3621 | 6626 | 90 | 6568 | 2235 | 1963 | 87.8300 | |
| mlin-fermikit | INDEL | D1_5 | HG002compoundhet | * | 74.1830 | 69.7262 | 79.2484 | 64.3487 | 8531 | 3704 | 8520 | 2231 | 2171 | 97.3106 | |
| qzeng-custom | INDEL | D16_PLUS | * | het | 80.5778 | 97.4992 | 68.6613 | 61.3602 | 3080 | 79 | 4888 | 2231 | 308 | 13.8055 | |