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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39001-39050 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.4468 | 99.1471 | 95.8038 | 68.8013 | 3836 | 33 | 3790 | 166 | 160 | 96.3855 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0330 | 98.6660 | 99.4027 | 68.8043 | 1997 | 27 | 1997 | 12 | 2 | 16.6667 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 92.9577 | 89.1892 | 97.0588 | 68.8073 | 33 | 4 | 33 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 68.8073 | 68 | 0 | 68 | 0 | 0 | ||
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 48.0237 | 81.0651 | 34.1176 | 68.8073 | 137 | 32 | 58 | 112 | 111 | 99.1071 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.8422 | 99.9434 | 92.0643 | 68.8076 | 1766 | 1 | 1775 | 153 | 105 | 68.6275 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.0016 | 90.9261 | 95.1741 | 68.8082 | 1944 | 194 | 1913 | 97 | 35 | 36.0825 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 85.0092 | 76.6467 | 95.4198 | 68.8095 | 128 | 39 | 125 | 6 | 5 | 83.3333 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 62.5303 | 57.6923 | 68.2540 | 68.8119 | 15 | 11 | 43 | 20 | 12 | 60.0000 | |
| hfeng-pmm1 | SNP | ti | map_l125_m1_e0 | * | 99.4515 | 99.2091 | 99.6951 | 68.8149 | 29103 | 232 | 29099 | 89 | 25 | 28.0899 | |
| dgrover-gatk | SNP | ti | map_l100_m1_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 68.8172 | 29 | 0 | 29 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | map_l125_m2_e0 | homalt | 98.0723 | 96.4102 | 99.7927 | 68.8173 | 5801 | 216 | 5778 | 12 | 9 | 75.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.6383 | 94.3878 | 96.9223 | 68.8174 | 2035 | 121 | 2047 | 65 | 13 | 20.0000 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5825 | 99.3750 | 99.7908 | 68.8193 | 1431 | 9 | 1431 | 3 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D6_15 | HG002compoundhet | het | 89.9917 | 98.0140 | 83.1832 | 68.8202 | 839 | 17 | 831 | 168 | 166 | 98.8095 | |
| jli-custom | SNP | ti | map_l125_m1_e0 | het | 99.1158 | 98.8065 | 99.4270 | 68.8246 | 18048 | 218 | 18046 | 104 | 33 | 31.7308 | |
| cchapple-custom | SNP | ti | map_l150_m2_e1 | homalt | 98.1938 | 96.4643 | 99.9865 | 68.8251 | 7421 | 272 | 7418 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | ti | map_siren | het | 96.2259 | 94.0079 | 98.5512 | 68.8261 | 58644 | 3738 | 58635 | 862 | 83 | 9.6288 | |
| gduggal-bwafb | SNP | tv | map_l125_m1_e0 | homalt | 99.4861 | 99.1126 | 99.8624 | 68.8267 | 5808 | 52 | 5808 | 8 | 6 | 75.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.9773 | 97.5806 | 98.3773 | 68.8271 | 968 | 24 | 970 | 16 | 5 | 31.2500 | |
| jlack-gatk | INDEL | I16_PLUS | HG002complexvar | hetalt | 94.5436 | 90.1493 | 99.3884 | 68.8275 | 302 | 33 | 325 | 2 | 1 | 50.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.1077 | 97.3988 | 98.8270 | 68.8300 | 337 | 9 | 337 | 4 | 1 | 25.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 24.4790 | 14.1603 | 90.2314 | 68.8301 | 258 | 1564 | 351 | 38 | 31 | 81.5789 | |
| ciseli-custom | SNP | ti | map_l100_m1_e0 | hetalt | 75.4717 | 68.9655 | 83.3333 | 68.8312 | 20 | 9 | 20 | 4 | 4 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 71.6574 | 56.6038 | 97.6190 | 68.8312 | 330 | 253 | 328 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.3063 | 96.6102 | 98.0125 | 68.8327 | 2565 | 90 | 2515 | 51 | 39 | 76.4706 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.8863 | 96.6892 | 99.1133 | 68.8334 | 2570 | 88 | 2571 | 23 | 22 | 95.6522 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.0047 | 98.3051 | 99.7143 | 68.8335 | 348 | 6 | 349 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.5706 | 70.3775 | 91.5264 | 68.8371 | 3300 | 1389 | 3316 | 307 | 18 | 5.8632 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | het | 89.1342 | 98.1308 | 81.6487 | 68.8379 | 840 | 16 | 832 | 187 | 185 | 98.9305 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.3220 | 99.7917 | 98.8568 | 68.8391 | 1437 | 3 | 1470 | 17 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7622 | 99.7519 | 99.7725 | 68.8442 | 4825 | 12 | 4825 | 11 | 7 | 63.6364 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 43.9926 | 38.2022 | 51.8519 | 68.8462 | 68 | 110 | 84 | 78 | 56 | 71.7949 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 62.9804 | 73.2283 | 55.2486 | 68.8468 | 93 | 34 | 100 | 81 | 11 | 13.5802 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.2829 | 94.9045 | 97.7021 | 68.8472 | 894 | 48 | 1233 | 29 | 19 | 65.5172 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 93.3962 | 88.3929 | 99.0000 | 68.8474 | 99 | 13 | 99 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | * | map_l125_m2_e0 | * | 99.3286 | 99.1032 | 99.5549 | 68.8474 | 46304 | 419 | 46301 | 207 | 67 | 32.3671 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.1732 | 94.9348 | 95.4128 | 68.8499 | 3861 | 206 | 3848 | 185 | 153 | 82.7027 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.3957 | 100.0000 | 96.8421 | 68.8525 | 92 | 0 | 92 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 1.8111 | 0.9524 | 18.4211 | 68.8525 | 7 | 728 | 7 | 31 | 22 | 70.9677 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.0000 | 99.0847 | 98.9155 | 68.8533 | 1732 | 16 | 1733 | 19 | 12 | 63.1579 | |
| qzeng-custom | SNP | * | map_siren | het | 92.1648 | 86.4602 | 98.6753 | 68.8551 | 78671 | 12320 | 77914 | 1046 | 710 | 67.8776 | |
| egarrison-hhga | SNP | tv | map_l125_m1_e0 | het | 99.1809 | 98.6569 | 99.7105 | 68.8561 | 9990 | 136 | 9990 | 29 | 12 | 41.3793 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.1165 | 95.7477 | 98.5251 | 68.8562 | 5359 | 238 | 5344 | 80 | 71 | 88.7500 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e0 | * | 98.9313 | 98.0912 | 99.7860 | 68.8564 | 31244 | 608 | 31247 | 67 | 22 | 32.8358 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e0 | homalt | 98.7568 | 97.7231 | 99.8125 | 68.8568 | 5880 | 137 | 5857 | 11 | 9 | 81.8182 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9859 | 98.8636 | 99.1085 | 68.8570 | 2001 | 23 | 2001 | 18 | 6 | 33.3333 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.2861 | 96.5348 | 98.0492 | 68.8578 | 2563 | 92 | 2513 | 50 | 38 | 76.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.3503 | 99.2642 | 99.4366 | 68.8610 | 11467 | 85 | 11472 | 65 | 58 | 89.2308 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.3503 | 99.2642 | 99.4366 | 68.8610 | 11467 | 85 | 11472 | 65 | 58 | 89.2308 | |