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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
37801-37850 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | I6_15 | HG002complexvar | homalt | 84.4108 | 80.1483 | 89.1522 | 51.9071 | 973 | 241 | 978 | 119 | 99 | 83.1933 | |
| ciseli-custom | SNP | tv | map_siren | het | 84.4100 | 82.1595 | 86.7874 | 65.3031 | 23505 | 5104 | 23489 | 3576 | 93 | 2.6007 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.4065 | 96.1747 | 75.2044 | 56.2444 | 3721 | 148 | 4416 | 1456 | 1419 | 97.4588 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 84.4037 | 73.2095 | 99.6390 | 55.5377 | 828 | 303 | 828 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.4015 | 97.2145 | 74.5726 | 47.8842 | 349 | 10 | 349 | 119 | 117 | 98.3193 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 84.4004 | 74.5748 | 97.2080 | 44.1952 | 6095 | 2078 | 6093 | 175 | 173 | 98.8571 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m1_e0 | * | 84.3978 | 75.4533 | 95.7480 | 93.2533 | 541 | 176 | 608 | 27 | 23 | 85.1852 | |
| anovak-vg | SNP | ti | map_l100_m1_e0 | * | 84.3963 | 88.5106 | 80.6475 | 68.7475 | 42424 | 5507 | 42052 | 10091 | 2274 | 22.5349 | |
| jlack-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | het | 84.3889 | 91.6667 | 78.1818 | 96.3648 | 44 | 4 | 43 | 12 | 4 | 33.3333 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m1_e0 | het | 84.3881 | 76.1411 | 94.6387 | 94.4659 | 367 | 115 | 406 | 23 | 19 | 82.6087 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3874 | 97.5345 | 74.3636 | 48.4035 | 8189 | 207 | 8676 | 2991 | 2903 | 97.0578 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e1 | het | 84.3869 | 73.7420 | 98.6235 | 86.5752 | 11753 | 4185 | 11750 | 164 | 1 | 0.6098 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.3860 | 83.9286 | 84.8485 | 77.2727 | 141 | 27 | 140 | 25 | 23 | 92.0000 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 84.3810 | 94.8490 | 75.9939 | 75.6668 | 31524 | 1712 | 31558 | 9969 | 9887 | 99.1775 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 84.3756 | 73.2446 | 99.4960 | 78.1450 | 991 | 362 | 987 | 5 | 3 | 60.0000 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m1_e0 | homalt | 84.3750 | 84.3750 | 84.3750 | 86.7220 | 54 | 10 | 54 | 10 | 10 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 84.3750 | 77.1429 | 93.1034 | 76.8000 | 27 | 8 | 27 | 2 | 1 | 50.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.3708 | 77.0533 | 93.2238 | 41.8507 | 910 | 271 | 908 | 66 | 66 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.3679 | 93.1480 | 77.1005 | 68.0245 | 3317 | 244 | 3377 | 1003 | 177 | 17.6471 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 84.3637 | 87.9716 | 81.0401 | 48.2088 | 3218 | 440 | 3257 | 762 | 318 | 41.7323 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.3571 | 94.2901 | 76.3174 | 88.4761 | 1222 | 74 | 1231 | 382 | 52 | 13.6126 | |
| qzeng-custom | INDEL | D6_15 | map_l150_m2_e1 | * | 84.3557 | 82.3529 | 86.4583 | 93.8184 | 70 | 15 | 83 | 13 | 6 | 46.1538 | |
| ckim-gatk | SNP | * | map_l150_m1_e0 | het | 84.3543 | 74.8499 | 96.6237 | 89.7210 | 14458 | 4858 | 14452 | 505 | 40 | 7.9208 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 84.3537 | 73.8095 | 98.4127 | 62.2754 | 62 | 22 | 62 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | map_l125_m1_e0 | het | 84.3537 | 96.8750 | 74.6988 | 93.2134 | 62 | 2 | 62 | 21 | 19 | 90.4762 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002compoundhet | * | 84.3510 | 75.2217 | 96.0024 | 42.9312 | 1612 | 531 | 1585 | 66 | 64 | 96.9697 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 84.3407 | 95.6876 | 75.3996 | 74.3623 | 29800 | 1343 | 30092 | 9818 | 643 | 6.5492 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 84.3407 | 95.6876 | 75.3996 | 74.3623 | 29800 | 1343 | 30092 | 9818 | 643 | 6.5492 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 84.3374 | 74.7117 | 96.8102 | 79.6075 | 3628 | 1228 | 3642 | 120 | 34 | 28.3333 | |
| mlin-fermikit | INDEL | I1_5 | segdup | hetalt | 84.3373 | 72.9167 | 100.0000 | 94.9791 | 35 | 13 | 36 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 84.3373 | 86.0656 | 82.6772 | 96.9962 | 105 | 17 | 105 | 22 | 2 | 9.0909 | |
| anovak-vg | SNP | * | map_l100_m2_e1 | * | 84.3316 | 88.9439 | 80.1741 | 71.0026 | 66474 | 8263 | 65661 | 16237 | 3582 | 22.0607 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 84.3305 | 80.0000 | 89.1566 | 86.2583 | 76 | 19 | 74 | 9 | 4 | 44.4444 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 84.3287 | 99.4131 | 73.2189 | 85.2401 | 847 | 5 | 853 | 312 | 168 | 53.8462 | |
| jpowers-varprowl | INDEL | D6_15 | HG002complexvar | homalt | 84.3192 | 79.7263 | 89.4737 | 58.7771 | 932 | 237 | 935 | 110 | 93 | 84.5455 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 84.3168 | 83.7696 | 84.8712 | 76.9763 | 800 | 155 | 791 | 141 | 92 | 65.2482 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 84.3152 | 73.5419 | 98.7866 | 76.1775 | 1387 | 499 | 1384 | 17 | 13 | 76.4706 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 84.3152 | 93.7856 | 76.5821 | 40.7415 | 2143 | 142 | 2142 | 655 | 651 | 99.3893 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m2_e0 | het | 84.3060 | 98.2490 | 73.8286 | 91.1437 | 505 | 9 | 646 | 229 | 52 | 22.7074 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e0 | het | 84.3040 | 73.6198 | 98.6157 | 86.5798 | 11615 | 4162 | 11612 | 163 | 1 | 0.6135 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3015 | 79.4055 | 89.8409 | 68.3211 | 748 | 194 | 734 | 83 | 52 | 62.6506 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.2998 | 74.7038 | 96.7245 | 58.1245 | 15386 | 5210 | 15385 | 521 | 324 | 62.1881 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.2971 | 80.2083 | 88.8252 | 77.8834 | 308 | 76 | 310 | 39 | 36 | 92.3077 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.2914 | 83.4336 | 85.1671 | 70.9828 | 31623 | 6279 | 32286 | 5623 | 5042 | 89.6674 | |
| ckim-isaac | INDEL | * | map_l100_m2_e1 | het | 84.2890 | 73.9650 | 97.9626 | 86.2811 | 1733 | 610 | 1731 | 36 | 15 | 41.6667 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| mlin-fermikit | SNP | ti | map_siren | * | 84.2869 | 75.7361 | 95.0143 | 45.5372 | 76005 | 24350 | 76001 | 3988 | 3501 | 87.7884 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 84.2857 | 75.1592 | 95.9350 | 54.2751 | 118 | 39 | 118 | 5 | 2 | 40.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 84.2832 | 73.2558 | 99.2188 | 72.2343 | 126 | 46 | 127 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 84.2828 | 78.0622 | 91.5805 | 48.9211 | 3110 | 874 | 3100 | 285 | 235 | 82.4561 | |