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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11301-11350 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | map_siren | * | 97.9969 | 97.3279 | 98.6752 | 85.5636 | 7212 | 198 | 7225 | 97 | 19 | 19.5876 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | * | 95.5217 | 95.2157 | 95.8298 | 35.3889 | 2229 | 112 | 2229 | 97 | 95 | 97.9381 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9598 | 98.5931 | 99.3293 | 80.6409 | 14366 | 205 | 14366 | 97 | 14 | 14.4330 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9598 | 98.5931 | 99.3293 | 80.6409 | 14366 | 205 | 14366 | 97 | 14 | 14.4330 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 93.1476 | 88.3677 | 98.4741 | 26.6190 | 6085 | 801 | 6260 | 97 | 90 | 92.7835 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 80.6824 | 72.6236 | 90.7531 | 35.9976 | 955 | 360 | 952 | 97 | 93 | 95.8763 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 85.1218 | 85.4985 | 84.7484 | 72.4437 | 566 | 96 | 539 | 97 | 47 | 48.4536 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.7696 | 99.8855 | 99.6539 | 55.1919 | 27927 | 32 | 27926 | 97 | 8 | 8.2474 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.7394 | 94.9841 | 92.5270 | 73.6767 | 1193 | 63 | 1201 | 97 | 62 | 63.9175 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.3802 | 93.5166 | 99.4246 | 60.9201 | 16429 | 1139 | 16588 | 96 | 15 | 15.6250 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.2282 | 99.3586 | 97.1232 | 68.6872 | 3253 | 21 | 3241 | 96 | 93 | 96.8750 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e1 | * | 96.4393 | 96.0449 | 96.8369 | 94.4522 | 2137 | 88 | 2939 | 96 | 68 | 70.8333 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8591 | 96.7290 | 96.9897 | 63.1840 | 3105 | 105 | 3093 | 96 | 93 | 96.8750 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2755 | 99.4715 | 99.0802 | 50.4204 | 10352 | 55 | 10341 | 96 | 89 | 92.7083 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 77.7513 | 65.3494 | 95.9630 | 64.1921 | 2282 | 1210 | 2282 | 96 | 29 | 30.2083 | |
| gduggal-bwaplat | SNP | tv | map_l100_m1_e0 | * | 80.7967 | 68.0462 | 99.4275 | 83.4681 | 16672 | 7829 | 16673 | 96 | 19 | 19.7917 | |
| gduggal-bwaplat | SNP | tv | map_l100_m1_e0 | het | 84.9313 | 74.2687 | 99.1687 | 85.9377 | 11450 | 3967 | 11452 | 96 | 19 | 19.7917 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 73.5287 | 71.5370 | 75.6345 | 65.0089 | 377 | 150 | 298 | 96 | 96 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 90.6327 | 87.6737 | 93.7984 | 45.3197 | 1451 | 204 | 1452 | 96 | 90 | 93.7500 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 45.1634 | 29.5192 | 96.0848 | 46.1217 | 921 | 2199 | 2356 | 96 | 96 | 100.0000 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e1 | het | 56.1207 | 39.2931 | 98.1570 | 69.2394 | 5114 | 7901 | 5113 | 96 | 5 | 5.2083 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 66.6667 | 100.0000 | 50.0000 | 60.4938 | 22 | 0 | 96 | 96 | 85 | 88.5417 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 77.6408 | 64.0764 | 98.4903 | 40.8685 | 6712 | 3763 | 6263 | 96 | 86 | 89.5833 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 97.4206 | 97.7525 | 97.0909 | 66.2577 | 3175 | 73 | 3204 | 96 | 3 | 3.1250 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.3248 | 99.2165 | 99.4333 | 71.0574 | 16842 | 133 | 16845 | 96 | 85 | 88.5417 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.6238 | 92.9702 | 96.3373 | 84.5241 | 2526 | 191 | 2525 | 96 | 61 | 63.5417 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.3248 | 99.2165 | 99.4333 | 71.0574 | 16842 | 133 | 16845 | 96 | 85 | 88.5417 | |
| ckim-gatk | INDEL | * | map_l150_m2_e0 | het | 94.2693 | 98.5651 | 90.3323 | 93.9690 | 893 | 13 | 897 | 96 | 6 | 6.2500 | |
| ckim-gatk | INDEL | * | map_l150_m2_e1 | het | 94.3211 | 98.4848 | 90.4950 | 93.9981 | 910 | 14 | 914 | 96 | 6 | 6.2500 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.3047 | 90.1065 | 86.5734 | 76.6949 | 592 | 65 | 619 | 96 | 50 | 52.0833 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.8668 | 98.5050 | 86.0668 | 52.0529 | 593 | 9 | 593 | 96 | 87 | 90.6250 | |
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 95.6540 | 95.4293 | 95.8798 | 35.4392 | 2234 | 107 | 2234 | 96 | 94 | 97.9167 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2803 | 99.4811 | 99.0803 | 50.1719 | 10353 | 54 | 10342 | 96 | 88 | 91.6667 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8994 | 99.2682 | 96.5678 | 63.0857 | 2713 | 20 | 2701 | 96 | 92 | 95.8333 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 45.4545 | 89.5238 | 0 | 0 | 80 | 96 | 28 | 29.1667 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 23.7665 | 14.5247 | 65.3430 | 41.4376 | 191 | 1124 | 181 | 96 | 38 | 39.5833 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | * | 99.4486 | 99.1930 | 99.7055 | 58.6476 | 32451 | 264 | 32505 | 96 | 76 | 79.1667 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.0868 | 99.0968 | 99.0767 | 50.8276 | 10313 | 94 | 10302 | 96 | 89 | 92.7083 | |
| jli-custom | SNP | ti | map_l150_m2_e0 | * | 99.2101 | 98.8933 | 99.5289 | 73.1343 | 20285 | 227 | 20283 | 96 | 36 | 37.5000 | |
| hfeng-pmm3 | SNP | * | map_l150_m0_e0 | * | 99.1727 | 99.1439 | 99.2015 | 79.7142 | 11929 | 103 | 11926 | 96 | 9 | 9.3750 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.4040 | 89.7684 | 97.3466 | 51.5533 | 3527 | 402 | 3522 | 96 | 90 | 93.7500 | |
| hfeng-pmm2 | SNP | ti | map_l150_m0_e0 | het | 98.5736 | 98.9994 | 98.1514 | 83.2987 | 5046 | 51 | 5044 | 95 | 8 | 8.4211 | |
| ckim-gatk | INDEL | * | map_l150_m1_e0 | het | 93.9968 | 98.4795 | 89.9044 | 93.5685 | 842 | 13 | 846 | 95 | 6 | 6.3158 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2867 | 99.8758 | 98.7045 | 36.9692 | 7238 | 9 | 7238 | 95 | 94 | 98.9474 | |
| ciseli-custom | INDEL | * | map_l150_m0_e0 | het | 64.8517 | 61.2903 | 68.8525 | 95.2903 | 209 | 132 | 210 | 95 | 45 | 47.3684 | |
| qzeng-custom | INDEL | * | map_l100_m2_e1 | homalt | 85.5777 | 78.8447 | 93.5680 | 81.7812 | 1010 | 271 | 1382 | 95 | 15 | 15.7895 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e0 | het | 55.8942 | 39.0731 | 98.1471 | 68.9855 | 5033 | 7848 | 5032 | 95 | 5 | 5.2632 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.1641 | 99.7099 | 96.6655 | 41.7144 | 2750 | 8 | 2754 | 95 | 83 | 87.3684 | |