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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73001-73050 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | INDEL | D16_PLUS | * | homalt | 98.7698 | 99.6454 | 97.9094 | 70.3716 | 1686 | 6 | 1686 | 36 | 27 | 75.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.3386 | 99.5196 | 97.1853 | 74.6230 | 1243 | 6 | 1243 | 36 | 27 | 75.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.3386 | 99.5196 | 97.1853 | 74.6230 | 1243 | 6 | 1243 | 36 | 27 | 75.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.8506 | 94.9010 | 98.8819 | 51.0518 | 2829 | 152 | 2830 | 32 | 27 | 84.3750 | |
| bgallagher-sentieon | SNP | tv | map_siren | het | 99.3778 | 99.6714 | 99.0859 | 61.4179 | 28515 | 94 | 28510 | 263 | 27 | 10.2662 | |
| rpoplin-dv42 | SNP | tv | map_l250_m2_e0 | het | 97.8098 | 97.8351 | 97.7846 | 87.2638 | 1898 | 42 | 1898 | 43 | 27 | 62.7907 | |
| rpoplin-dv42 | SNP | * | map_l100_m0_e0 | homalt | 99.3564 | 98.9759 | 99.7398 | 62.7443 | 11501 | 119 | 11501 | 30 | 27 | 90.0000 | |
| rpoplin-dv42 | SNP | * | map_l250_m0_e0 | * | 97.4806 | 96.9555 | 98.0114 | 92.0139 | 2070 | 65 | 2070 | 42 | 27 | 64.2857 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e0 | * | 97.9477 | 97.5088 | 98.3906 | 98.2302 | 3601 | 92 | 3607 | 59 | 27 | 45.7627 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002complexvar | homalt | 99.8477 | 99.8959 | 99.7995 | 52.5914 | 13434 | 14 | 13438 | 27 | 27 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7835 | 87.9479 | 98.1818 | 64.9979 | 1620 | 222 | 1620 | 30 | 27 | 90.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.9010 | 100.0000 | 95.8884 | 72.2268 | 653 | 0 | 653 | 28 | 27 | 96.4286 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.5412 | 99.5261 | 88.2353 | 68.7254 | 210 | 1 | 210 | 28 | 27 | 96.4286 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.8162 | 92.9554 | 98.8588 | 48.8601 | 2771 | 210 | 2772 | 32 | 27 | 84.3750 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1514 | 90.4452 | 98.1743 | 66.8941 | 1666 | 176 | 1667 | 31 | 27 | 87.0968 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4494 | 99.3637 | 99.5353 | 61.3550 | 55277 | 354 | 55266 | 258 | 27 | 10.4651 | |
| 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 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | * | 97.6446 | 97.6263 | 97.6630 | 66.8096 | 1604 | 39 | 1588 | 38 | 27 | 71.0526 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 79.4104 | 79.0850 | 79.7386 | 67.5159 | 121 | 32 | 122 | 31 | 27 | 87.0968 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2969 | 92.1490 | 96.5473 | 61.2007 | 2993 | 255 | 3020 | 108 | 27 | 25.0000 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.9052 | 96.1507 | 99.7250 | 58.1999 | 10491 | 420 | 10518 | 29 | 27 | 93.1034 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4203 | 98.9214 | 95.9641 | 68.3987 | 642 | 7 | 642 | 27 | 27 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.6923 | 100.0000 | 91.7404 | 70.4446 | 311 | 0 | 311 | 28 | 27 | 96.4286 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6743 | 99.8742 | 99.4753 | 60.5238 | 55561 | 70 | 55550 | 293 | 27 | 9.2150 | |
| dgrover-gatk | SNP | tv | map_l125_m1_e0 | * | 99.2231 | 99.2882 | 99.1581 | 73.2603 | 15902 | 114 | 15900 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e0 | * | 99.2454 | 99.3086 | 99.1822 | 74.7468 | 16375 | 114 | 16373 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e1 | * | 99.2530 | 99.3156 | 99.1905 | 74.7864 | 16543 | 114 | 16541 | 135 | 27 | 20.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.2951 | 97.8471 | 98.7472 | 84.7253 | 3545 | 78 | 3547 | 45 | 27 | 60.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2155 | 98.8292 | 99.6047 | 53.9964 | 17642 | 209 | 17640 | 70 | 27 | 38.5714 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 88.1005 | 80.0000 | 98.0263 | 81.2243 | 428 | 107 | 1341 | 27 | 27 | 100.0000 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 72.1154 | 94.9392 | 0 | 0 | 75 | 29 | 27 | 93.1034 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 93.9099 | 89.5234 | 98.7484 | 34.7140 | 2273 | 266 | 2288 | 29 | 28 | 96.5517 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4319 | 99.1366 | 99.7290 | 37.0539 | 18026 | 157 | 18031 | 49 | 28 | 57.1429 | |
| egarrison-hhga | SNP | * | map_l125_m1_e0 | het | 99.2263 | 98.7039 | 99.7544 | 69.9636 | 28024 | 368 | 28024 | 69 | 28 | 40.5797 | |
| egarrison-hhga | SNP | * | map_l125_m2_e0 | het | 99.2355 | 98.7312 | 99.7450 | 71.3586 | 28946 | 372 | 28946 | 74 | 28 | 37.8378 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | het | 99.2353 | 98.7314 | 99.7444 | 71.4034 | 29264 | 376 | 29264 | 75 | 28 | 37.3333 | |
| egarrison-hhga | SNP | tv | HG002complexvar | het | 99.7360 | 99.5170 | 99.9560 | 21.2359 | 150003 | 728 | 150023 | 66 | 28 | 42.4242 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | homalt | 99.1596 | 99.2326 | 99.0866 | 43.1871 | 3362 | 26 | 3363 | 31 | 28 | 90.3226 | |
| eyeh-varpipe | INDEL | * | map_l125_m0_e0 | * | 96.5567 | 96.2585 | 96.8567 | 95.6158 | 849 | 33 | 1325 | 43 | 28 | 65.1163 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 84.0816 | 96.2647 | 0 | 0 | 206 | 39 | 28 | 71.7949 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.0391 | 99.4096 | 96.7059 | 82.8744 | 1347 | 8 | 1233 | 42 | 28 | 66.6667 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5453 | 100.0000 | 91.4706 | 70.3833 | 311 | 0 | 311 | 29 | 28 | 96.5517 | |
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | het | 76.6298 | 73.5321 | 80.0000 | 57.0120 | 814 | 293 | 488 | 122 | 28 | 22.9508 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.0457 | 84.6445 | 98.4943 | 38.8914 | 2679 | 486 | 2682 | 41 | 28 | 68.2927 | |