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 | |||||||||||||||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 66.0556 | 65.0014 | 67.1446 | 72.1458 | 2355 | 1268 | 3278 | 1604 | 1089 | 67.8928 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7082 | 95.6585 | 99.8477 | 51.9462 | 3305 | 150 | 3279 | 5 | 4 | 80.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.5353 | 76.8626 | 89.1121 | 55.4494 | 3126 | 941 | 3282 | 401 | 398 | 99.2519 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.2878 | 93.9576 | 98.7365 | 52.3236 | 3281 | 211 | 3282 | 42 | 37 | 88.0952 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.9560 | 96.0290 | 95.8832 | 44.2273 | 3313 | 137 | 3284 | 141 | 11 | 7.8014 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 91.6132 | 84.5897 | 99.9088 | 64.9616 | 3288 | 599 | 3285 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | HG002compoundhet | homalt | 98.5034 | 97.1370 | 99.9088 | 42.9389 | 3291 | 97 | 3286 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.7955 | 92.0590 | 99.8481 | 42.7080 | 3246 | 280 | 3287 | 5 | 4 | 80.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.7955 | 92.0590 | 99.8481 | 42.7080 | 3246 | 280 | 3287 | 5 | 4 | 80.0000 | |
| ciseli-custom | SNP | tv | map_l100_m0_e0 | homalt | 86.8291 | 85.5694 | 88.1265 | 64.0732 | 3291 | 555 | 3288 | 443 | 348 | 78.5553 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 55.3475 | 87.7323 | 40.4253 | 50.7774 | 3304 | 462 | 3289 | 4847 | 4536 | 93.5837 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 55.3475 | 87.7323 | 40.4253 | 50.7774 | 3304 | 462 | 3289 | 4847 | 4536 | 93.5837 | |
| gduggal-snapfb | INDEL | D1_5 | * | hetalt | 84.1984 | 78.0771 | 91.3611 | 79.2100 | 7999 | 2246 | 3289 | 311 | 140 | 45.0161 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.5587 | 96.4058 | 98.7395 | 42.1025 | 3326 | 124 | 3290 | 42 | 14 | 33.3333 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.3822 | 94.2153 | 98.6511 | 52.7880 | 3290 | 202 | 3291 | 45 | 38 | 84.4444 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5660 | 94.2153 | 99.0370 | 52.3174 | 3290 | 202 | 3291 | 32 | 26 | 81.2500 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | * | 93.4753 | 91.3274 | 95.7267 | 83.9230 | 3275 | 311 | 3293 | 147 | 38 | 25.8503 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | homalt | 60.4067 | 43.2904 | 99.9090 | 85.1344 | 3297 | 4319 | 3293 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 53.1638 | 65.0431 | 44.9536 | 49.5979 | 1282 | 689 | 3296 | 4036 | 3328 | 82.4579 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 92.0493 | 86.2286 | 98.7126 | 25.5959 | 3281 | 524 | 3297 | 43 | 35 | 81.3953 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 74.2485 | 93.1298 | 61.7328 | 60.2144 | 1586 | 117 | 3299 | 2045 | 1364 | 66.6993 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5751 | 94.4731 | 98.7728 | 51.8310 | 3299 | 193 | 3300 | 41 | 34 | 82.9268 | |
| asubramanian-gatk | SNP | tv | map_l100_m2_e1 | homalt | 52.3802 | 35.4870 | 99.9697 | 82.0942 | 3301 | 6001 | 3301 | 1 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | D1_5 | map_siren | * | 93.7516 | 95.1544 | 92.3895 | 83.9860 | 3358 | 171 | 3302 | 272 | 95 | 34.9265 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.6054 | 94.5304 | 98.7736 | 51.8161 | 3301 | 191 | 3302 | 41 | 34 | 82.9268 | |
| ltrigg-rtg1 | SNP | tv | HG002compoundhet | homalt | 99.0027 | 98.2290 | 99.7886 | 40.4282 | 3328 | 60 | 3304 | 7 | 1 | 14.2857 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | homalt | 98.7009 | 97.5502 | 99.8791 | 43.2979 | 3305 | 83 | 3304 | 4 | 3 | 75.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_siren | * | 94.5668 | 93.7093 | 95.4401 | 81.4755 | 3307 | 222 | 3307 | 158 | 114 | 72.1519 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 80.7660 | 81.6777 | 79.8745 | 42.7070 | 3330 | 747 | 3310 | 834 | 461 | 55.2758 | |
| jpowers-varprowl | INDEL | * | map_l100_m2_e0 | * | 91.3432 | 89.7373 | 93.0076 | 85.5055 | 3314 | 379 | 3312 | 249 | 199 | 79.9197 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.2496 | 92.7964 | 99.9698 | 39.4554 | 3272 | 254 | 3312 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.2496 | 92.7964 | 99.9698 | 39.4554 | 3272 | 254 | 3312 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | HG002complexvar | * | 77.4674 | 68.9900 | 88.3200 | 51.9231 | 3306 | 1486 | 3312 | 438 | 187 | 42.6941 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 82.0473 | 70.6121 | 97.9019 | 63.3528 | 3311 | 1378 | 3313 | 71 | 11 | 15.4930 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2162 | 95.0172 | 99.5194 | 52.2792 | 3318 | 174 | 3313 | 16 | 11 | 68.7500 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.3156 | 74.9046 | 75.7313 | 50.0285 | 2943 | 986 | 3314 | 1062 | 550 | 51.7891 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.4868 | 81.5589 | 85.5080 | 68.6930 | 3317 | 750 | 3316 | 562 | 522 | 92.8826 | |
| eyeh-varpipe | INDEL | I1_5 | map_siren | * | 96.0860 | 95.6406 | 96.5357 | 78.7530 | 2874 | 131 | 3316 | 119 | 92 | 77.3109 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.5706 | 70.3775 | 91.5264 | 68.8371 | 3300 | 1389 | 3316 | 307 | 18 | 5.8632 | |
| gduggal-snapplat | SNP | tv | map_l100_m0_e0 | homalt | 92.5848 | 86.1934 | 100.0000 | 67.9954 | 3315 | 531 | 3316 | 0 | 0 | ||
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8891 | 94.9885 | 98.8674 | 52.9255 | 3317 | 175 | 3317 | 38 | 38 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 53.7340 | 37.1777 | 96.8750 | 57.0119 | 2192 | 3704 | 3317 | 107 | 99 | 92.5234 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 53.7340 | 37.1777 | 96.8750 | 57.0119 | 2192 | 3704 | 3317 | 107 | 99 | 92.5234 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e1 | * | 92.1115 | 87.8860 | 96.7638 | 96.1058 | 3301 | 455 | 3319 | 111 | 17 | 15.3153 | |
| eyeh-varpipe | INDEL | I6_15 | HG002complexvar | * | 76.1535 | 69.3656 | 84.4139 | 46.8082 | 3324 | 1468 | 3320 | 613 | 606 | 98.8581 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 91.8726 | 90.2567 | 93.5475 | 72.9167 | 3270 | 353 | 3320 | 229 | 219 | 95.6332 | |
| ghariani-varprowl | INDEL | * | map_l100_m1_e0 | * | 90.4036 | 92.6380 | 88.2744 | 91.8947 | 3322 | 264 | 3320 | 441 | 203 | 46.0317 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | homalt | 99.4361 | 98.9079 | 99.9699 | 40.5831 | 3351 | 37 | 3321 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9663 | 95.1890 | 98.8113 | 52.9502 | 3324 | 168 | 3325 | 40 | 33 | 82.5000 | |