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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6051-6100 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | * | 84.5768 | 85.6111 | 83.5671 | 84.5427 | 1660 | 279 | 1668 | 328 | 123 | 37.5000 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.8529 | 82.0562 | 83.6653 | 62.9041 | 1724 | 377 | 1680 | 328 | 287 | 87.5000 | |
| bgallagher-sentieon | INDEL | I1_5 | HG002compoundhet | homalt | 66.5990 | 99.6960 | 50.0000 | 87.6390 | 328 | 1 | 328 | 328 | 328 | 100.0000 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 97.5583 | 98.0061 | 97.1145 | 57.2508 | 10863 | 221 | 11039 | 328 | 130 | 39.6341 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.6411 | 98.1762 | 97.1119 | 60.4037 | 10712 | 199 | 11029 | 328 | 130 | 39.6341 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 38.4615 | 88.9511 | 0 | 0 | 205 | 328 | 43 | 13.1098 | |
| ciseli-custom | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 21.3429 | 95.1903 | 0 | 0 | 89 | 328 | 84 | 25.6098 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 81.4502 | 90.3104 | 74.1732 | 79.4532 | 960 | 103 | 942 | 328 | 70 | 21.3415 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 83.5759 | 89.6241 | 78.2925 | 40.0872 | 1192 | 138 | 1183 | 328 | 283 | 86.2805 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 73.1064 | 82.4147 | 65.6873 | 70.7937 | 628 | 134 | 626 | 327 | 81 | 24.7706 | |
| anovak-vg | INDEL | I1_5 | map_siren | het | 46.4738 | 35.8715 | 65.9729 | 86.5236 | 603 | 1078 | 634 | 327 | 82 | 25.0765 | |
| 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 | |
| astatham-gatk | INDEL | I6_15 | HG002compoundhet | * | 94.7145 | 93.3113 | 96.1606 | 37.2227 | 8189 | 587 | 8190 | 327 | 325 | 99.3884 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 94.0198 | 99.8511 | 88.8320 | 71.0242 | 2682 | 4 | 2601 | 327 | 6 | 1.8349 | |
| qzeng-custom | SNP | ti | HG002complexvar | homalt | 99.2303 | 98.6432 | 99.8245 | 18.6252 | 190839 | 2625 | 186005 | 327 | 247 | 75.5352 | |
| qzeng-custom | SNP | tv | map_l125_m2_e0 | * | 85.0368 | 75.4382 | 97.4343 | 83.5735 | 12439 | 4050 | 12418 | 327 | 274 | 83.7920 | |
| jpowers-varprowl | SNP | tv | map_l150_m2_e0 | het | 95.7712 | 96.0287 | 95.5150 | 83.3577 | 6964 | 288 | 6964 | 327 | 76 | 23.2416 | |
| hfeng-pmm2 | INDEL | * | HG002compoundhet | het | 86.3875 | 82.5598 | 90.5872 | 78.6150 | 3380 | 714 | 3147 | 327 | 317 | 96.9419 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m1_e0 | * | 63.5476 | 57.9537 | 70.3367 | 84.8997 | 776 | 563 | 773 | 326 | 278 | 85.2761 | |
| ckim-dragen | SNP | * | map_l150_m0_e0 | het | 96.9776 | 97.9975 | 95.9788 | 84.1657 | 7781 | 159 | 7781 | 326 | 26 | 7.9755 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1837 | 96.7573 | 97.6138 | 51.8740 | 13338 | 447 | 13336 | 326 | 319 | 97.8528 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.3850 | 94.7826 | 88.2225 | 88.3133 | 2507 | 138 | 2442 | 326 | 84 | 25.7669 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.0147 | 91.6982 | 94.3696 | 64.0306 | 5578 | 505 | 5464 | 326 | 313 | 96.0123 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3157 | 96.8617 | 97.7740 | 53.9248 | 14321 | 464 | 14319 | 326 | 316 | 96.9325 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4585 | 97.1390 | 97.7802 | 53.9739 | 14362 | 423 | 14360 | 326 | 315 | 96.6258 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 34.3511 | 83.3333 | 21.6346 | 92.3048 | 85 | 17 | 90 | 326 | 5 | 1.5337 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.3550 | 97.1312 | 95.5910 | 44.3893 | 7144 | 211 | 7068 | 326 | 14 | 4.2945 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 28.5833 | 18.1471 | 67.2691 | 61.6333 | 713 | 3216 | 670 | 326 | 173 | 53.0675 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 23.1120 | 18.1529 | 31.7992 | 75.7484 | 171 | 771 | 152 | 326 | 3 | 0.9202 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 22.5601 | 18.5079 | 28.8840 | 55.7171 | 129 | 568 | 132 | 325 | 240 | 73.8462 | |
| qzeng-custom | SNP | tv | map_l100_m2_e1 | het | 88.6428 | 81.2273 | 97.5483 | 82.6203 | 12946 | 2992 | 12931 | 325 | 244 | 75.0769 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.5231 | 92.2277 | 96.9357 | 58.1370 | 3726 | 314 | 10281 | 325 | 271 | 83.3846 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.1220 | 97.1827 | 99.0797 | 47.1607 | 15316 | 444 | 34988 | 325 | 263 | 80.9231 | |
| jlack-gatk | SNP | * | map_l250_m0_e0 | * | 91.3907 | 96.9555 | 86.4301 | 95.6372 | 2070 | 65 | 2070 | 325 | 28 | 8.6154 | |
| dgrover-gatk | SNP | * | map_l100_m1_e0 | het | 99.3755 | 99.4665 | 99.2846 | 70.4056 | 45117 | 242 | 45106 | 325 | 62 | 19.0769 | |
| eyeh-varpipe | INDEL | * | HG002compoundhet | hetalt | 52.4540 | 35.9293 | 97.1234 | 60.7545 | 9047 | 16133 | 10973 | 325 | 315 | 96.9231 | |
| gduggal-bwavard | INDEL | D16_PLUS | HG002complexvar | het | 81.5892 | 88.8889 | 75.3974 | 65.5091 | 984 | 123 | 996 | 325 | 263 | 80.9231 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 51.6345 | 52.3810 | 50.9091 | 64.2857 | 330 | 300 | 336 | 324 | 243 | 75.0000 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e0 | * | 84.6007 | 85.6397 | 83.5866 | 84.4811 | 1640 | 275 | 1650 | 324 | 122 | 37.6543 | |
| raldana-dualsentieon | SNP | * | map_l150_m1_e0 | het | 98.5115 | 98.6954 | 98.3283 | 76.6149 | 19064 | 252 | 19058 | 324 | 3 | 0.9259 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 53.5399 | 39.1005 | 84.8881 | 55.0336 | 1817 | 2830 | 1820 | 324 | 282 | 87.0370 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 93.2273 | 96.9246 | 89.8017 | 74.7396 | 2868 | 91 | 2853 | 324 | 8 | 2.4691 | |
| gduggal-snapfb | SNP | ti | map_l150_m0_e0 | het | 94.2863 | 94.8597 | 93.7197 | 77.7514 | 4835 | 262 | 4835 | 324 | 174 | 53.7037 | |
| qzeng-custom | SNP | tv | map_l100_m2_e0 | het | 88.5810 | 81.1371 | 97.5288 | 82.6321 | 12801 | 2976 | 12787 | 324 | 244 | 75.3086 | |
| ltrigg-rtg2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4820 | 99.5452 | 99.4189 | 54.5520 | 55378 | 253 | 55428 | 324 | 26 | 8.0247 | |
| ltrigg-rtg2 | SNP | * | HG002complexvar | het | 99.8358 | 99.7414 | 99.9305 | 18.3888 | 464296 | 1204 | 464515 | 323 | 94 | 29.1022 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 94.3311 | 97.1963 | 91.6300 | 59.5874 | 3536 | 102 | 3536 | 323 | 127 | 39.3189 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 74.5853 | 86.8721 | 65.3433 | 69.9161 | 761 | 115 | 609 | 323 | 321 | 99.3808 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 76.8360 | 71.2348 | 83.3933 | 72.7285 | 1523 | 615 | 1622 | 323 | 129 | 39.9381 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.4006 | 94.8267 | 92.0168 | 79.6069 | 3831 | 209 | 3723 | 323 | 189 | 58.5139 | |