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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
47551-47600 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.7336 | 97.7570 | 99.7300 | 68.1488 | 28068 | 644 | 28068 | 76 | 5 | 6.5790 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.7336 | 97.7570 | 99.7300 | 68.1488 | 28068 | 644 | 28068 | 76 | 5 | 6.5790 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 92.1348 | 89.1304 | 95.3488 | 68.1481 | 41 | 5 | 41 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | * | het | 94.6145 | 93.4143 | 95.8459 | 68.1424 | 2539 | 179 | 2538 | 110 | 63 | 57.2727 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e1 | het | 97.4111 | 98.0685 | 96.7625 | 68.1401 | 30362 | 598 | 30366 | 1016 | 436 | 42.9134 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3671 | 100.0000 | 98.7421 | 68.1363 | 157 | 0 | 157 | 2 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | D16_PLUS | * | * | 60.4248 | 56.9575 | 64.3415 | 68.1361 | 3864 | 2920 | 3874 | 2147 | 2111 | 98.3232 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.0835 | 99.8396 | 92.5998 | 68.1347 | 2490 | 4 | 2365 | 189 | 7 | 3.7037 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.9360 | 95.2617 | 96.6200 | 68.1344 | 5569 | 277 | 5517 | 193 | 187 | 96.8912 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.9360 | 95.2617 | 96.6200 | 68.1344 | 5569 | 277 | 5517 | 193 | 187 | 96.8912 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 51.4209 | 36.9403 | 84.5736 | 68.1324 | 2178 | 3718 | 2182 | 398 | 329 | 82.6633 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 51.4209 | 36.9403 | 84.5736 | 68.1324 | 2178 | 3718 | 2182 | 398 | 329 | 82.6633 | |
| astatham-gatk | SNP | ti | map_l100_m1_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 68.1319 | 29 | 0 | 29 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | * | het | 95.1311 | 91.7586 | 98.7610 | 68.1314 | 2494 | 224 | 2471 | 31 | 8 | 25.8065 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 83.9976 | 93.6170 | 76.1708 | 68.1299 | 572 | 39 | 553 | 173 | 168 | 97.1098 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.9766 | 99.6958 | 96.3156 | 68.1284 | 2950 | 9 | 2954 | 113 | 5 | 4.4248 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3508 | 99.3647 | 99.3369 | 68.1260 | 3128 | 20 | 3146 | 21 | 3 | 14.2857 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 95.4385 | 99.6385 | 91.5782 | 68.1251 | 1378 | 5 | 1381 | 127 | 8 | 6.2992 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3103 | 100.0000 | 98.6301 | 68.1223 | 216 | 0 | 216 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 41.1620 | 27.4615 | 82.1429 | 68.1214 | 410 | 1083 | 414 | 90 | 76 | 84.4444 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 93.3333 | 91.3043 | 95.4545 | 68.1159 | 42 | 4 | 42 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 53.5912 | 38.5935 | 87.6543 | 68.1102 | 225 | 358 | 71 | 10 | 10 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6815 | 97.8712 | 99.5052 | 68.1063 | 3816 | 83 | 3821 | 19 | 14 | 73.6842 | |
| ckim-isaac | SNP | * | map_l150_m0_e0 | homalt | 62.3254 | 45.2922 | 99.8921 | 68.1060 | 1852 | 2237 | 1852 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 45.1741 | 82.9268 | 31.0421 | 68.1047 | 136 | 28 | 140 | 311 | 310 | 99.6785 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6301 | 100.0000 | 97.2973 | 68.1034 | 36 | 0 | 36 | 1 | 1 | 100.0000 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.1948 | 98.5039 | 99.8954 | 68.1029 | 9547 | 145 | 9547 | 10 | 9 | 90.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2668 | 99.4808 | 99.0537 | 68.1013 | 3257 | 17 | 3245 | 31 | 29 | 93.5484 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1966 | 96.0492 | 98.3718 | 68.1010 | 17115 | 704 | 16736 | 277 | 229 | 82.6715 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.9227 | 92.3913 | 95.5056 | 68.1004 | 85 | 7 | 85 | 4 | 3 | 75.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.2276 | 93.3190 | 95.1542 | 68.0956 | 433 | 31 | 432 | 22 | 16 | 72.7273 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 56.7944 | 80.4054 | 43.9024 | 68.0934 | 119 | 29 | 108 | 138 | 138 | 100.0000 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 72.2413 | 99.3100 | 56.7681 | 68.0924 | 2159 | 15 | 2164 | 1648 | 10 | 0.6068 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 28.2195 | 16.6235 | 93.3071 | 68.0905 | 321 | 1610 | 474 | 34 | 33 | 97.0588 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 28.2195 | 16.6235 | 93.3071 | 68.0905 | 321 | 1610 | 474 | 34 | 33 | 97.0588 | |
| gduggal-bwafb | SNP | * | map_l125_m1_e0 | homalt | 99.4923 | 99.1127 | 99.8748 | 68.0895 | 16755 | 150 | 16755 | 21 | 13 | 61.9048 | |
| ltrigg-rtg1 | SNP | ti | map_l150_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 68.0851 | 15 | 0 | 15 | 0 | 0 | ||
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9781 | 96.7532 | 97.2039 | 68.0840 | 596 | 20 | 591 | 17 | 15 | 88.2353 | |
| gduggal-bwavard | INDEL | D1_5 | HG002compoundhet | * | 18.6118 | 15.4230 | 23.4630 | 68.0839 | 1887 | 10348 | 1786 | 5826 | 5576 | 95.7089 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e0 | het | 97.3939 | 98.0537 | 96.7430 | 68.0809 | 30026 | 596 | 30030 | 1011 | 436 | 43.1256 | |
| bgallagher-sentieon | SNP | ti | map_l150_m1_e0 | homalt | 99.6923 | 99.5087 | 99.8767 | 68.0791 | 7291 | 36 | 7291 | 9 | 7 | 77.7778 | |
| hfeng-pmm3 | SNP | * | map_l100_m0_e0 | * | 99.4850 | 99.4123 | 99.5578 | 68.0774 | 32648 | 193 | 32644 | 145 | 21 | 14.4828 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0012 | 96.8927 | 99.1354 | 68.0773 | 343 | 11 | 344 | 3 | 3 | 100.0000 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 68.0618 | 59.5506 | 79.4118 | 68.0751 | 53 | 36 | 54 | 14 | 14 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.5532 | 99.4766 | 99.6299 | 68.0748 | 3231 | 17 | 3230 | 12 | 5 | 41.6667 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.5254 | 99.5254 | 99.5254 | 68.0722 | 9646 | 46 | 9646 | 46 | 24 | 52.1739 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.5574 | 92.1147 | 99.2674 | 68.0702 | 257 | 22 | 271 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.4591 | 98.7277 | 98.1920 | 68.0700 | 3492 | 45 | 16727 | 308 | 247 | 80.1948 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 72.3623 | 57.5758 | 97.3684 | 68.0672 | 38 | 28 | 37 | 1 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 77.3737 | 66.0300 | 93.4236 | 68.0667 | 484 | 249 | 483 | 34 | 28 | 82.3529 | |