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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5251-5300 / 86044 show all | |||||||||||||||
| raldana-dualsentieon | SNP | ti | HG002complexvar | het | 99.8369 | 99.6928 | 99.9815 | 16.7345 | 313799 | 967 | 313748 | 58 | 9 | 15.5172 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1110 | 97.3601 | 98.8735 | 45.3846 | 35626 | 966 | 45291 | 516 | 450 | 87.2093 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 22.4034 | 18.2049 | 29.1188 | 44.6643 | 215 | 966 | 228 | 555 | 520 | 93.6937 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 84.8287 | 79.2124 | 91.3021 | 39.5276 | 3681 | 966 | 1753 | 167 | 81 | 48.5030 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 1.0256 | 0.0000 | 0.0000 | 10 | 965 | 0 | 0 | 0 | ||
| gduggal-snapfb | SNP | ti | map_l125_m1_e0 | * | 96.8890 | 96.7104 | 97.0682 | 71.9792 | 28370 | 965 | 28374 | 857 | 408 | 47.6079 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.6406 | 75.4390 | 91.3622 | 46.4432 | 2964 | 965 | 3226 | 305 | 294 | 96.3934 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 85.1837 | 88.4652 | 82.1369 | 53.6130 | 7401 | 965 | 7403 | 1610 | 1503 | 93.3540 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 81.4677 | 70.5559 | 96.3720 | 80.0416 | 2310 | 964 | 2311 | 87 | 48 | 55.1724 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 58.4872 | 85.5667 | 44.4273 | 41.2283 | 5715 | 964 | 5748 | 7190 | 7163 | 99.6245 | |
| ckim-dragen | SNP | ti | * | * | 99.8327 | 99.9538 | 99.7120 | 20.2602 | 2084547 | 964 | 2084816 | 6022 | 378 | 6.2770 | |
| jlack-gatk | INDEL | I6_15 | HG002compoundhet | * | 90.8429 | 89.0155 | 92.7469 | 37.7522 | 7812 | 964 | 7813 | 611 | 606 | 99.1817 | |
| ghariani-varprowl | SNP | * | HG002compoundhet | het | 84.6682 | 93.2007 | 77.5669 | 61.4559 | 13214 | 964 | 13447 | 3889 | 29 | 0.7457 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.0349 | 98.5054 | 99.5702 | 72.8907 | 63468 | 963 | 63480 | 274 | 249 | 90.8759 | |
| jlack-gatk | INDEL | D1_5 | HG002compoundhet | * | 93.7462 | 92.1291 | 95.4211 | 64.7145 | 11272 | 963 | 11274 | 541 | 497 | 91.8669 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.7796 | 27.0106 | 45.0758 | 47.5149 | 356 | 962 | 357 | 435 | 415 | 95.4023 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 70.4680 | 75.1615 | 66.3261 | 61.3642 | 2908 | 961 | 3246 | 1648 | 1139 | 69.1141 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e1 | homalt | 93.2871 | 87.5211 | 99.8663 | 73.9142 | 6733 | 960 | 6724 | 9 | 9 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 88.6540 | 89.8499 | 87.4895 | 45.7726 | 8498 | 960 | 9343 | 1336 | 702 | 52.5449 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 78.0161 | 64.7448 | 98.1308 | 54.0773 | 1763 | 960 | 105 | 2 | 2 | 100.0000 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 0.0000 | 0 | 959 | 0 | 0 | 0 | |||
| ckim-isaac | SNP | tv | map_l250_m1_e0 | het | 63.1820 | 46.3346 | 99.2806 | 91.7792 | 828 | 959 | 828 | 6 | 1 | 16.6667 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 40.5868 | 37.3203 | 44.4800 | 81.8709 | 571 | 959 | 556 | 694 | 384 | 55.3314 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 40.5868 | 37.3203 | 44.4800 | 81.8709 | 571 | 959 | 556 | 694 | 384 | 55.3314 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.2083 | 0.1043 | 100.0000 | 0.0000 | 1 | 958 | 1 | 0 | 0 | ||
| cchapple-custom | SNP | * | HG002complexvar | homalt | 99.8273 | 99.6680 | 99.9871 | 18.5601 | 287616 | 958 | 286343 | 37 | 32 | 86.4865 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.7656 | 94.6334 | 98.9961 | 51.3619 | 16893 | 958 | 17059 | 173 | 13 | 7.5145 | |
| ckim-isaac | SNP | ti | map_l250_m2_e0 | homalt | 62.2886 | 45.2830 | 99.7481 | 85.1339 | 792 | 957 | 792 | 2 | 2 | 100.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 88.4071 | 84.2391 | 93.0089 | 52.2708 | 5115 | 957 | 5122 | 385 | 278 | 72.2078 | |
| jlack-gatk | INDEL | I6_15 | * | hetalt | 94.0319 | 88.8083 | 99.9084 | 39.1561 | 7594 | 957 | 7635 | 7 | 6 | 85.7143 | |
| jlack-gatk | INDEL | I6_15 | HG002compoundhet | hetalt | 94.0390 | 88.7900 | 99.9475 | 29.7817 | 7580 | 957 | 7621 | 4 | 4 | 100.0000 | |
| jli-custom | INDEL | * | HG002complexvar | * | 99.2454 | 98.7574 | 99.7382 | 56.8994 | 75982 | 956 | 75827 | 199 | 151 | 75.8794 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.4523 | 93.1870 | 99.9548 | 33.8499 | 13076 | 956 | 13269 | 6 | 5 | 83.3333 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 56.6050 | 50.5432 | 64.3189 | 53.8060 | 977 | 956 | 968 | 537 | 532 | 99.0689 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 67.7028 | 91.6754 | 53.6688 | 45.2639 | 10528 | 956 | 14570 | 12578 | 12360 | 98.2668 | |
| ckim-vqsr | INDEL | D1_5 | * | * | 99.5124 | 99.3485 | 99.6767 | 61.5493 | 145789 | 956 | 145843 | 473 | 318 | 67.2304 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | * | 94.7676 | 92.2629 | 97.4120 | 66.1892 | 11400 | 956 | 11405 | 303 | 301 | 99.3399 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 62.8376 | 94.6349 | 47.0342 | 60.4447 | 16863 | 956 | 16945 | 19082 | 18800 | 98.5222 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 69.4728 | 78.5200 | 62.2951 | 44.9448 | 3491 | 955 | 7334 | 4439 | 3996 | 90.0203 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.6799 | 93.0581 | 98.4538 | 59.4166 | 12802 | 955 | 19039 | 299 | 108 | 36.1204 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.6799 | 93.0581 | 98.4538 | 59.4166 | 12802 | 955 | 19039 | 299 | 108 | 36.1204 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 36.0348 | 0.0000 | 0.0000 | 538 | 955 | 0 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | * | het | 99.5204 | 99.5086 | 99.5323 | 62.3713 | 193179 | 954 | 192796 | 906 | 561 | 61.9205 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 58.0207 | 41.0019 | 99.1935 | 43.8406 | 663 | 954 | 615 | 5 | 5 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | * | * | 87.3801 | 85.9375 | 88.8720 | 69.7132 | 5830 | 954 | 5846 | 732 | 623 | 85.1093 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 30.1078 | 27.6176 | 33.0916 | 63.8123 | 364 | 954 | 365 | 738 | 734 | 99.4580 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 76.4238 | 95.1325 | 63.8642 | 77.1773 | 18626 | 953 | 18983 | 10741 | 319 | 2.9699 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 76.4238 | 95.1325 | 63.8642 | 77.1773 | 18626 | 953 | 18983 | 10741 | 319 | 2.9699 | |