PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79851-79900 / 86044 show all | |||||||||||||||
| gduggal-bwafb | SNP | ti | map_siren | het | 99.0568 | 99.3219 | 98.7930 | 59.4400 | 61959 | 423 | 61963 | 757 | 131 | 17.3052 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.5437 | 77.6835 | 97.6853 | 56.4907 | 6499 | 1867 | 6499 | 154 | 131 | 85.0649 | |
| gduggal-bwaplat | INDEL | D6_15 | * | hetalt | 82.8017 | 71.8008 | 97.7833 | 50.4460 | 5869 | 2305 | 5867 | 133 | 131 | 98.4962 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 83.0248 | 72.2847 | 97.5133 | 68.6969 | 6043 | 2317 | 6039 | 154 | 132 | 85.7143 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 83.0248 | 72.2847 | 97.5133 | 68.6969 | 6043 | 2317 | 6039 | 154 | 132 | 85.7143 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002compoundhet | * | 84.8012 | 75.3988 | 96.8828 | 44.4562 | 6617 | 2159 | 6620 | 213 | 132 | 61.9718 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 81.2553 | 73.6695 | 90.5826 | 44.2627 | 8181 | 2924 | 2068 | 215 | 132 | 61.3953 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 46.3373 | 71.5686 | 34.2593 | 33.5385 | 73 | 29 | 74 | 142 | 132 | 92.9577 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 88.6180 | 82.8379 | 95.2651 | 48.0962 | 3205 | 664 | 2857 | 142 | 132 | 92.9577 | |
| eyeh-varpipe | INDEL | I1_5 | * | hetalt | 60.5783 | 43.9661 | 97.3679 | 73.2444 | 4922 | 6273 | 5216 | 141 | 132 | 93.6170 | |
| mlin-fermikit | SNP | * | map_l250_m0_e0 | * | 40.4330 | 27.1194 | 79.4239 | 82.2628 | 579 | 1556 | 579 | 150 | 132 | 88.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 78.1075 | 64.7471 | 98.4152 | 46.2255 | 10816 | 5889 | 10060 | 162 | 132 | 81.4815 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | * | 88.7656 | 86.9142 | 90.6977 | 68.5511 | 1428 | 215 | 1443 | 148 | 132 | 89.1892 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 78.1075 | 64.7471 | 98.4152 | 46.2255 | 10816 | 5889 | 10060 | 162 | 132 | 81.4815 | |
| ciseli-custom | INDEL | * | map_l150_m2_e0 | het | 66.9093 | 62.8035 | 71.5895 | 93.6451 | 569 | 337 | 572 | 227 | 132 | 58.1498 | |
| ckim-isaac | INDEL | * | HG002complexvar | homalt | 93.1685 | 88.5818 | 98.2561 | 47.1228 | 23941 | 3086 | 23890 | 424 | 132 | 31.1321 | |
| ckim-gatk | INDEL | D6_15 | * | homalt | 98.8810 | 99.8735 | 97.9079 | 55.6525 | 6318 | 8 | 6318 | 135 | 132 | 97.7778 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.1861 | 99.8938 | 96.5358 | 60.0431 | 3762 | 4 | 3762 | 135 | 132 | 97.7778 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.1861 | 99.8938 | 96.5358 | 60.0431 | 3762 | 4 | 3762 | 135 | 132 | 97.7778 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3820 | 97.9096 | 98.8590 | 53.4408 | 5480 | 117 | 13083 | 151 | 132 | 87.4172 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.4801 | 83.0652 | 88.0396 | 45.1406 | 981 | 200 | 979 | 133 | 132 | 99.2481 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 72.9935 | 63.5053 | 85.8149 | 62.8966 | 837 | 481 | 853 | 141 | 132 | 93.6170 | |
| ckim-isaac | INDEL | I1_5 | HG002compoundhet | homalt | 68.0851 | 72.9483 | 63.8298 | 82.4627 | 240 | 89 | 240 | 136 | 132 | 97.0588 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 78.0049 | 67.7625 | 91.8950 | 70.9693 | 1278 | 608 | 1610 | 142 | 132 | 92.9577 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2978 | 94.0048 | 98.7055 | 32.8581 | 9847 | 628 | 10599 | 139 | 132 | 94.9640 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.9630 | 95.2537 | 80.0000 | 69.7438 | 582 | 29 | 548 | 137 | 132 | 96.3504 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 18.8667 | 23.9437 | 15.5660 | 65.0165 | 17 | 54 | 33 | 179 | 132 | 73.7430 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | het | 88.7434 | 85.9865 | 91.6830 | 94.7245 | 2798 | 456 | 2800 | 254 | 132 | 51.9685 | |
| gduggal-snapplat | SNP | tv | map_l150_m0_e0 | het | 88.2289 | 86.2117 | 90.3428 | 90.9621 | 2451 | 392 | 2451 | 262 | 132 | 50.3817 | |
| gduggal-snapvard | INDEL | * | map_l150_m1_e0 | het | 82.1183 | 96.2573 | 71.6010 | 91.6254 | 823 | 32 | 1127 | 447 | 132 | 29.5302 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0489 | 99.3034 | 98.7958 | 56.9516 | 11404 | 80 | 11404 | 139 | 132 | 94.9640 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.5891 | 97.0144 | 98.1706 | 67.3997 | 29570 | 910 | 29515 | 550 | 132 | 24.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.5891 | 97.0144 | 98.1706 | 67.3997 | 29570 | 910 | 29515 | 550 | 132 | 24.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2969 | 95.1533 | 99.5393 | 51.1225 | 36065 | 1837 | 36299 | 168 | 133 | 79.1667 | |
| anovak-vg | SNP | * | map_l100_m2_e0 | homalt | 91.7943 | 85.3141 | 99.3397 | 61.4498 | 23481 | 4042 | 23170 | 154 | 133 | 86.3636 | |
| anovak-vg | SNP | * | map_l100_m2_e1 | homalt | 91.8309 | 85.3756 | 99.3422 | 61.4163 | 23731 | 4065 | 23410 | 155 | 133 | 85.8065 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 78.9511 | 85.2645 | 73.5081 | 83.3082 | 677 | 117 | 813 | 293 | 133 | 45.3925 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.1397 | 99.2867 | 95.0836 | 54.6384 | 2784 | 20 | 2785 | 144 | 133 | 92.3611 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.3969 | 99.2733 | 95.5900 | 55.8480 | 3142 | 23 | 3143 | 145 | 133 | 91.7241 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7120 | 95.2896 | 98.1776 | 52.4952 | 5462 | 270 | 7542 | 140 | 133 | 95.0000 | |
| astatham-gatk | INDEL | D6_15 | * | homalt | 98.8889 | 99.8893 | 97.9083 | 55.4989 | 6319 | 7 | 6319 | 135 | 133 | 98.5185 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.1994 | 99.9203 | 96.5367 | 59.9507 | 3763 | 3 | 3763 | 135 | 133 | 98.5185 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.1994 | 99.9203 | 96.5367 | 59.9507 | 3763 | 3 | 3763 | 135 | 133 | 98.5185 | |
| cchapple-custom | INDEL | D16_PLUS | * | het | 96.8499 | 96.8344 | 96.8654 | 63.8824 | 3059 | 100 | 5068 | 164 | 133 | 81.0976 | |
| cchapple-custom | INDEL | D6_15 | * | homalt | 98.7463 | 99.6364 | 97.8720 | 46.7949 | 6303 | 23 | 6255 | 136 | 133 | 97.7941 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | * | 97.1628 | 97.8613 | 96.4743 | 69.7586 | 23977 | 524 | 23970 | 876 | 133 | 15.1826 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | het | 96.2530 | 98.0346 | 94.5349 | 73.9009 | 15114 | 303 | 15153 | 876 | 133 | 15.1826 | |
| cchapple-custom | SNP | tv | map_l100_m2_e0 | * | 97.1975 | 97.9028 | 96.5023 | 71.7198 | 24508 | 525 | 24500 | 888 | 133 | 14.9775 | |
| cchapple-custom | SNP | tv | map_l100_m2_e0 | het | 96.2979 | 98.0731 | 94.5857 | 75.5847 | 15473 | 304 | 15513 | 888 | 133 | 14.9775 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.6391 | 99.8632 | 97.4447 | 51.1732 | 5110 | 7 | 5110 | 134 | 133 | 99.2537 | |