PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73401-73450 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | D1_5 | HG002compoundhet | hetalt | 93.3119 | 88.0482 | 99.2450 | 76.1026 | 8995 | 1221 | 3549 | 27 | 27 | 100.0000 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 44.1015 | 42.1796 | 46.2069 | 48.7496 | 2241 | 3072 | 3551 | 4134 | 3627 | 87.7358 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 82.0492 | 96.8053 | 71.1966 | 41.3611 | 2212 | 73 | 3552 | 1437 | 1234 | 85.8733 | |
| gduggal-snapplat | INDEL | * | map_siren | het | 79.1743 | 73.0923 | 86.3603 | 90.4763 | 3295 | 1213 | 3552 | 561 | 54 | 9.6257 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.9814 | 83.6479 | 76.6228 | 91.4225 | 3545 | 693 | 3553 | 1084 | 49 | 4.5203 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9775 | 89.0167 | 99.5238 | 40.0705 | 3404 | 420 | 3553 | 17 | 17 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.4707 | 95.9016 | 89.2767 | 52.5444 | 468 | 20 | 3555 | 427 | 343 | 80.3279 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 84.5148 | 96.2617 | 75.3230 | 67.9780 | 1751 | 68 | 3556 | 1165 | 308 | 26.4378 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 84.5148 | 96.2617 | 75.3230 | 67.9780 | 1751 | 68 | 3556 | 1165 | 308 | 26.4378 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1689 | 98.4332 | 99.9157 | 48.1800 | 3581 | 57 | 3556 | 3 | 2 | 66.6667 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | * | 96.0874 | 94.0096 | 98.2592 | 84.3618 | 3531 | 225 | 3556 | 63 | 22 | 34.9206 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.4559 | 95.1485 | 89.9115 | 78.4139 | 3844 | 196 | 3556 | 399 | 354 | 88.7218 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2661 | 92.8252 | 99.9719 | 25.4244 | 3532 | 273 | 3557 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e0 | * | 97.6394 | 96.3174 | 98.9983 | 79.7338 | 3557 | 136 | 3558 | 36 | 6 | 16.6667 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2944 | 92.8778 | 99.9719 | 25.4138 | 3534 | 271 | 3559 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | tv | map_l125_m1_e0 | homalt | 75.5546 | 60.7338 | 99.9438 | 75.6613 | 3559 | 2301 | 3559 | 2 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0819 | 89.2259 | 99.4969 | 40.1872 | 3412 | 412 | 3560 | 18 | 17 | 94.4444 | |
| jmaeng-gatk | SNP | tv | map_l125_m1_e0 | homalt | 75.6286 | 60.8191 | 99.9719 | 74.7843 | 3564 | 2296 | 3564 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.7998 | 77.2097 | 99.1101 | 56.3009 | 3564 | 1052 | 3564 | 32 | 5 | 15.6250 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.0591 | 87.6396 | 99.1931 | 21.1150 | 3531 | 498 | 3565 | 29 | 24 | 82.7586 | |
| ciseli-custom | INDEL | D16_PLUS | * | * | 59.6718 | 52.7860 | 68.6237 | 57.6195 | 3581 | 3203 | 3565 | 1630 | 1503 | 92.2086 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.4344 | 93.1143 | 100.0000 | 27.8227 | 3543 | 262 | 3567 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 56.3707 | 87.9455 | 41.4787 | 65.8135 | 3553 | 487 | 3568 | 5034 | 4915 | 97.6361 | |
| gduggal-bwafb | INDEL | D1_5 | * | hetalt | 93.2065 | 88.0527 | 99.0011 | 79.2540 | 9021 | 1224 | 3568 | 36 | 36 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 35.3007 | 32.2054 | 39.0543 | 51.0895 | 3569 | 7513 | 3568 | 5568 | 5531 | 99.3355 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1048 | 98.5238 | 99.6927 | 45.3838 | 3604 | 54 | 3568 | 11 | 2 | 18.1818 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3225 | 98.7905 | 99.8601 | 50.4916 | 3594 | 44 | 3570 | 5 | 3 | 60.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.6406 | 93.7451 | 99.7207 | 30.0781 | 3567 | 238 | 3570 | 10 | 10 | 100.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.2698 | 98.4163 | 96.1497 | 78.7844 | 3853 | 62 | 3571 | 143 | 49 | 34.2657 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 87.7886 | 91.4554 | 84.4045 | 45.0390 | 974 | 91 | 3572 | 660 | 647 | 98.0303 | |
| ckim-gatk | SNP | * | map_l125_m0_e0 | homalt | 69.4469 | 53.2181 | 99.9161 | 80.0469 | 3572 | 3140 | 3572 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.4300 | 93.8983 | 97.0125 | 53.6214 | 2493 | 162 | 3572 | 110 | 76 | 69.0909 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.5017 | 90.8883 | 94.1735 | 55.0486 | 3571 | 358 | 3572 | 221 | 201 | 90.9502 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.5793 | 94.7690 | 92.4191 | 52.4483 | 3569 | 197 | 3572 | 293 | 241 | 82.2526 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.5793 | 94.7690 | 92.4191 | 52.4483 | 3569 | 197 | 3572 | 293 | 241 | 82.2526 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.1010 | 77.3614 | 97.0668 | 59.1479 | 3571 | 1045 | 3574 | 108 | 9 | 8.3333 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e0 | * | 97.1833 | 96.6423 | 97.7304 | 89.4395 | 3569 | 124 | 3574 | 83 | 16 | 19.2771 | |
| astatham-gatk | INDEL | * | map_l100_m2_e1 | * | 96.5544 | 95.0745 | 98.0811 | 86.7793 | 3571 | 185 | 3578 | 70 | 18 | 25.7143 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 83.0702 | 98.1137 | 72.0266 | 52.1291 | 3589 | 69 | 3579 | 1390 | 1276 | 91.7986 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9102 | 91.2700 | 94.6103 | 54.6326 | 3586 | 343 | 3581 | 204 | 197 | 96.5686 | |
| cchapple-custom | INDEL | I6_15 | HG002complexvar | het | 98.1734 | 97.1975 | 99.1692 | 56.5725 | 2289 | 66 | 3581 | 30 | 25 | 83.3333 | |
| anovak-vg | INDEL | D6_15 | HG002complexvar | * | 72.7472 | 67.2954 | 79.1602 | 52.2024 | 3568 | 1734 | 3582 | 943 | 676 | 71.6861 | |
| 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 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1559 | 98.4882 | 99.8328 | 57.1769 | 3583 | 55 | 3583 | 6 | 4 | 66.6667 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.8816 | 95.9653 | 93.8220 | 79.5053 | 3877 | 163 | 3584 | 236 | 208 | 88.1356 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e1 | * | 97.3272 | 95.5005 | 99.2250 | 80.3823 | 3587 | 169 | 3585 | 28 | 7 | 25.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.9775 | 98.7855 | 99.1701 | 81.3679 | 3579 | 44 | 3585 | 30 | 6 | 20.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | * | * | 59.3408 | 53.1250 | 67.2039 | 51.2916 | 3604 | 3180 | 3586 | 1750 | 1709 | 97.6571 | |
| jmaeng-gatk | SNP | * | map_l125_m0_e0 | homalt | 69.6311 | 53.4267 | 99.9443 | 78.9757 | 3586 | 3126 | 3586 | 2 | 2 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e0 | * | 97.3112 | 96.9402 | 97.6852 | 97.7103 | 3580 | 113 | 3587 | 85 | 38 | 44.7059 | |