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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4751-4800 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 50.9371 | 34.6330 | 96.2465 | 52.9921 | 3846 | 7259 | 5436 | 212 | 205 | 96.6981 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | * | 81.7142 | 76.1213 | 88.1941 | 27.9899 | 1782 | 559 | 1763 | 236 | 205 | 86.8644 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.7858 | 90.4797 | 83.3817 | 76.0514 | 1226 | 129 | 1149 | 229 | 205 | 89.5197 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.1624 | 85.4630 | 88.9307 | 63.9481 | 1652 | 281 | 1655 | 206 | 205 | 99.5146 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 59.4656 | 87.5000 | 45.0363 | 57.4665 | 175 | 25 | 186 | 227 | 205 | 90.3084 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 26.2530 | 22.2973 | 31.9149 | 42.5829 | 33 | 115 | 105 | 224 | 205 | 91.5179 | |
| jpowers-varprowl | SNP | * | map_l150_m1_e0 | het | 96.1124 | 95.8014 | 96.4254 | 81.4447 | 18505 | 811 | 18505 | 686 | 205 | 29.8834 | |
| gduggal-snapplat | SNP | tv | map_l125_m0_e0 | het | 89.8264 | 88.7753 | 90.9027 | 88.4354 | 3907 | 494 | 3907 | 391 | 205 | 52.4297 | |
| gduggal-snapfb | SNP | tv | map_l125_m1_e0 | het | 96.2891 | 97.8866 | 94.7429 | 72.1296 | 9912 | 214 | 9912 | 550 | 205 | 37.2727 | |
| eyeh-varpipe | INDEL | D16_PLUS | HG002complexvar | homalt | 44.7304 | 49.8270 | 40.5797 | 45.3249 | 144 | 145 | 140 | 205 | 205 | 100.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1407 | 99.3309 | 96.9788 | 67.1842 | 35182 | 237 | 35277 | 1099 | 205 | 18.6533 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2164 | 97.1032 | 99.3555 | 50.5488 | 35532 | 1060 | 35455 | 230 | 205 | 89.1304 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4496 | 99.8356 | 99.0666 | 73.6565 | 21863 | 36 | 21863 | 206 | 205 | 99.5146 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.2568 | 87.6742 | 84.8845 | 71.5339 | 1195 | 168 | 1213 | 216 | 204 | 94.4444 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 94.1056 | 96.6465 | 91.6950 | 53.7560 | 3516 | 122 | 3511 | 318 | 204 | 64.1509 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.3782 | 98.4839 | 98.2727 | 72.8894 | 21567 | 332 | 21563 | 379 | 204 | 53.8259 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | het | 83.5782 | 74.2554 | 95.5781 | 89.7806 | 5385 | 1867 | 5382 | 249 | 204 | 81.9277 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 89.1201 | 81.4606 | 98.3693 | 34.9531 | 13608 | 3097 | 14116 | 234 | 204 | 87.1795 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 89.1201 | 81.4606 | 98.3693 | 34.9531 | 13608 | 3097 | 14116 | 234 | 204 | 87.1795 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9501 | 99.4036 | 98.5008 | 62.9678 | 15666 | 94 | 15506 | 236 | 204 | 86.4407 | |
| gduggal-bwavard | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.4880 | 97.6215 | 97.3548 | 60.2420 | 27294 | 665 | 27125 | 737 | 204 | 27.6798 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 85.2828 | 75.9897 | 97.1657 | 76.5450 | 7064 | 2232 | 7062 | 206 | 204 | 99.0291 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.6758 | 93.5408 | 95.8387 | 47.4428 | 1593 | 110 | 5988 | 260 | 204 | 78.4615 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 83.6519 | 73.9268 | 96.3233 | 56.4236 | 6992 | 2466 | 6995 | 267 | 204 | 76.4045 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.7010 | 96.5880 | 98.8399 | 43.3164 | 17636 | 623 | 17637 | 207 | 204 | 98.5507 | |
| gduggal-snapfb | INDEL | I1_5 | HG002compoundhet | hetalt | 85.0180 | 77.5969 | 94.0087 | 72.7861 | 8673 | 2504 | 4111 | 262 | 204 | 77.8626 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e1 | het | 87.7421 | 84.4985 | 91.2446 | 94.9087 | 4448 | 816 | 4450 | 427 | 204 | 47.7752 | |
| gduggal-snapplat | SNP | ti | HG002complexvar | homalt | 99.0919 | 98.3790 | 99.8152 | 19.4474 | 190328 | 3136 | 190130 | 352 | 203 | 57.6705 | |
| ghariani-varprowl | INDEL | * | map_l100_m1_e0 | * | 90.4036 | 92.6380 | 88.2744 | 91.8947 | 3322 | 264 | 3320 | 441 | 203 | 46.0317 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.8148 | 39.9386 | 77.9441 | 54.2466 | 780 | 1173 | 781 | 221 | 203 | 91.8552 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 68.4840 | 92.9334 | 54.2196 | 86.0939 | 2525 | 192 | 2602 | 2197 | 203 | 9.2399 | |
| qzeng-custom | SNP | tv | map_l150_m1_e0 | het | 83.1414 | 73.6683 | 95.4104 | 89.4270 | 5117 | 1829 | 5114 | 246 | 203 | 82.5203 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.8814 | 39.9386 | 78.2347 | 54.0553 | 780 | 1173 | 780 | 217 | 203 | 93.5484 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2219 | 99.3862 | 99.0582 | 74.4553 | 33032 | 204 | 33027 | 314 | 203 | 64.6497 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0722 | 99.3449 | 98.8011 | 64.3152 | 18047 | 119 | 18047 | 219 | 203 | 92.6941 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0722 | 99.3449 | 98.8011 | 64.3152 | 18047 | 119 | 18047 | 219 | 203 | 92.6941 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2661 | 91.3134 | 97.4160 | 66.6942 | 9198 | 875 | 9048 | 240 | 203 | 84.5833 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.3108 | 98.0414 | 98.5817 | 67.0115 | 17470 | 349 | 17099 | 246 | 203 | 82.5203 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 83.5091 | 84.3949 | 82.6418 | 67.4764 | 1060 | 196 | 1195 | 251 | 203 | 80.8765 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9340 | 99.3274 | 98.5437 | 62.8374 | 15654 | 106 | 15496 | 229 | 203 | 88.6463 | |
| egarrison-hhga | INDEL | D1_5 | * | homalt | 99.1875 | 99.1927 | 99.1824 | 59.4207 | 48531 | 395 | 48522 | 400 | 203 | 50.7500 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 82.2656 | 88.2213 | 77.0631 | 82.3781 | 1116 | 149 | 1270 | 378 | 203 | 53.7037 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| ckim-isaac | INDEL | * | HG002complexvar | hetalt | 77.5562 | 66.5856 | 92.8550 | 56.3369 | 2463 | 1236 | 3119 | 240 | 203 | 84.5833 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.1346 | 84.9322 | 98.3142 | 43.5277 | 13094 | 2323 | 13472 | 231 | 203 | 87.8788 | |
| ciseli-custom | INDEL | * | map_l100_m2_e0 | homalt | 69.5990 | 63.9968 | 76.2760 | 85.5956 | 807 | 454 | 807 | 251 | 203 | 80.8765 | |
| ciseli-custom | INDEL | * | map_l125_m2_e0 | het | 68.9335 | 65.4925 | 72.7562 | 91.5977 | 911 | 480 | 916 | 343 | 203 | 59.1837 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | * | 92.5060 | 86.7938 | 99.0230 | 59.4097 | 28957 | 4406 | 28886 | 285 | 203 | 71.2281 | |
| gduggal-bwafb | INDEL | D16_PLUS | * | homalt | 85.6946 | 83.9835 | 87.4769 | 60.7791 | 1421 | 271 | 1418 | 203 | 203 | 100.0000 | |