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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69851-69900 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 62.0445 | 67.3110 | 57.5423 | 47.2192 | 3935 | 1911 | 5947 | 4388 | 3469 | 79.0565 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 62.0445 | 67.3110 | 57.5423 | 47.2192 | 3935 | 1911 | 5947 | 4388 | 3469 | 79.0565 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.4653 | 94.4068 | 92.5425 | 38.8281 | 6971 | 413 | 14221 | 1146 | 906 | 79.0576 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.3454 | 95.7944 | 92.9397 | 77.9289 | 1435 | 63 | 1448 | 110 | 87 | 79.0909 | |
| mlin-fermikit | INDEL | * | map_l150_m2_e1 | * | 65.1571 | 52.8145 | 85.0279 | 85.1378 | 760 | 679 | 761 | 134 | 106 | 79.1045 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | * | 97.6899 | 96.4874 | 98.9228 | 68.1825 | 6153 | 224 | 6153 | 67 | 53 | 79.1045 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.1643 | 88.4244 | 98.4410 | 44.1529 | 12925 | 1692 | 27215 | 431 | 341 | 79.1183 | |
| ckim-isaac | SNP | ti | HG002compoundhet | * | 88.7627 | 82.1776 | 96.4952 | 32.6037 | 14363 | 3115 | 14647 | 532 | 421 | 79.1353 | |
| ckim-isaac | SNP | * | HG002complexvar | * | 95.9550 | 92.3552 | 99.8467 | 16.9098 | 696714 | 57671 | 697067 | 1070 | 847 | 79.1589 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.3317 | 95.2681 | 97.4194 | 82.1360 | 906 | 45 | 906 | 24 | 19 | 79.1667 | |
| ltrigg-rtg2 | INDEL | I1_5 | * | homalt | 99.7495 | 99.5797 | 99.9200 | 48.8836 | 60173 | 254 | 59955 | 48 | 38 | 79.1667 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5094 | 99.3762 | 99.6429 | 67.2531 | 6691 | 42 | 6696 | 24 | 19 | 79.1667 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 88.1449 | 83.3732 | 93.4959 | 66.1468 | 697 | 139 | 690 | 48 | 38 | 79.1667 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | homalt | 99.6081 | 99.3075 | 99.9106 | 57.8259 | 26816 | 187 | 26816 | 24 | 19 | 79.1667 | |
| astatham-gatk | SNP | * | map_l100_m2_e0 | homalt | 99.6137 | 99.3169 | 99.9123 | 60.3292 | 27335 | 188 | 27335 | 24 | 19 | 79.1667 | |
| astatham-gatk | SNP | * | map_l100_m2_e1 | homalt | 99.6157 | 99.3200 | 99.9131 | 60.3111 | 27607 | 189 | 27607 | 24 | 19 | 79.1667 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m0_e0 | het | 59.3607 | 61.3208 | 57.5221 | 94.3500 | 65 | 41 | 65 | 48 | 38 | 79.1667 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 17.8468 | 9.9840 | 84.0000 | 62.9630 | 125 | 1127 | 126 | 24 | 19 | 79.1667 | |
| gduggal-snapvard | SNP | ti | map_l125_m1_e0 | homalt | 97.8107 | 95.9258 | 99.7712 | 66.1153 | 10595 | 450 | 10464 | 24 | 19 | 79.1667 | |
| gduggal-snapvard | SNP | ti | map_l125_m2_e0 | homalt | 97.8264 | 95.9500 | 99.7776 | 68.4862 | 10898 | 460 | 10766 | 24 | 19 | 79.1667 | |
| gduggal-snapvard | SNP | ti | map_l125_m2_e1 | homalt | 97.8366 | 95.9679 | 99.7796 | 68.5265 | 10996 | 462 | 10863 | 24 | 19 | 79.1667 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 93.3264 | 87.6955 | 99.7299 | 56.2023 | 8859 | 1243 | 8863 | 24 | 19 | 79.1667 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.7527 | 75.1764 | 99.7922 | 61.3457 | 23125 | 7636 | 23046 | 48 | 38 | 79.1667 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0403 | 91.4014 | 98.9810 | 39.0442 | 2498 | 235 | 6994 | 72 | 57 | 79.1667 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2969 | 95.1533 | 99.5393 | 51.1225 | 36065 | 1837 | 36299 | 168 | 133 | 79.1667 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.1888 | 99.1803 | 95.2756 | 71.1364 | 484 | 4 | 484 | 24 | 19 | 79.1667 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | * | 99.4486 | 99.1930 | 99.7055 | 58.6476 | 32451 | 264 | 32505 | 96 | 76 | 79.1667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.0639 | 76.7320 | 97.9798 | 69.7941 | 1174 | 356 | 1164 | 24 | 19 | 79.1667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.0639 | 76.7320 | 97.9798 | 69.7941 | 1174 | 356 | 1164 | 24 | 19 | 79.1667 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | HG002complexvar | * | 94.7987 | 91.4790 | 98.3685 | 55.6259 | 1503 | 140 | 1447 | 24 | 19 | 79.1667 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | * | 97.4539 | 97.1695 | 97.7400 | 55.3894 | 31789 | 926 | 31787 | 735 | 582 | 79.1837 | |
| gduggal-snapvard | INDEL | D1_5 | * | * | 87.8248 | 91.1601 | 84.7249 | 55.7284 | 133771 | 12972 | 160064 | 28858 | 22853 | 79.1912 | |
| gduggal-bwaplat | INDEL | I1_5 | * | homalt | 95.8146 | 92.1560 | 99.7758 | 57.5165 | 55688 | 4740 | 55641 | 125 | 99 | 79.2000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3586 | 98.2333 | 98.4842 | 57.4113 | 6561 | 118 | 6562 | 101 | 80 | 79.2079 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | * | 33.1975 | 24.5225 | 51.3699 | 42.4631 | 321 | 988 | 300 | 284 | 225 | 79.2254 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.9533 | 97.9730 | 70.4362 | 86.4433 | 435 | 9 | 436 | 183 | 145 | 79.2350 | |
| jli-custom | SNP | ti | * | homalt | 99.9866 | 99.9797 | 99.9934 | 15.9268 | 802875 | 163 | 802870 | 53 | 42 | 79.2453 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 67.2776 | 57.7670 | 80.5369 | 88.2492 | 119 | 87 | 120 | 29 | 23 | 79.3103 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | homalt | 98.6152 | 97.3744 | 99.8881 | 60.4751 | 26294 | 709 | 25878 | 29 | 23 | 79.3103 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.2141 | 96.6855 | 97.7484 | 68.9339 | 2567 | 88 | 2518 | 58 | 46 | 79.3103 | |
| gduggal-snapvard | SNP | ti | map_l100_m0_e0 | homalt | 97.3605 | 95.2148 | 99.6052 | 63.3538 | 7402 | 372 | 7316 | 29 | 23 | 79.3103 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6877 | 98.2028 | 99.1775 | 66.2939 | 3497 | 64 | 3497 | 29 | 23 | 79.3103 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 16.9764 | 10.8209 | 39.3750 | 52.0958 | 58 | 478 | 63 | 97 | 77 | 79.3814 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 33.7398 | 28.1768 | 42.0398 | 49.5609 | 102 | 260 | 169 | 233 | 185 | 79.3991 | |
| ckim-vqsr | INDEL | I1_5 | * | * | 99.3579 | 99.0515 | 99.6662 | 59.3791 | 149235 | 1429 | 149282 | 500 | 397 | 79.4000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7836 | 84.1298 | 98.5804 | 37.3201 | 2359 | 445 | 2361 | 34 | 27 | 79.4118 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 91.0757 | 96.0870 | 86.5613 | 76.5524 | 221 | 9 | 219 | 34 | 27 | 79.4118 | |
| ghariani-varprowl | SNP | ti | HG002compoundhet | homalt | 92.9457 | 99.8242 | 86.9540 | 37.0935 | 7381 | 13 | 7385 | 1108 | 880 | 79.4224 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.1057 | 79.3599 | 89.4551 | 69.7220 | 1711 | 445 | 1773 | 209 | 166 | 79.4258 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 36.8196 | 27.4987 | 55.6992 | 44.8224 | 542 | 1429 | 1852 | 1473 | 1170 | 79.4297 | |