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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19551-19600 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.1080 | 90.6710 | 91.5493 | 68.5493 | 554 | 57 | 520 | 48 | 46 | 95.8333 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0975 | 98.5381 | 99.6632 | 66.5047 | 3842 | 57 | 3847 | 13 | 7 | 53.8462 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5254 | 97.4649 | 95.6039 | 64.9385 | 2153 | 56 | 2153 | 99 | 92 | 92.9293 | |
| hfeng-pmm2 | INDEL | * | map_l100_m1_e0 | * | 98.3031 | 98.4384 | 98.1682 | 84.3925 | 3530 | 56 | 3537 | 66 | 13 | 19.6970 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.0414 | 91.8486 | 96.3415 | 81.8634 | 631 | 56 | 632 | 24 | 14 | 58.3333 | |
| jlack-gatk | SNP | * | HG002compoundhet | het | 99.3003 | 99.6050 | 98.9974 | 47.5779 | 14122 | 56 | 14120 | 143 | 30 | 20.9790 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | het | 98.4241 | 97.9397 | 98.9135 | 73.5192 | 2662 | 56 | 2640 | 29 | 4 | 13.7931 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9134 | 97.1029 | 98.7375 | 60.0294 | 1877 | 56 | 1877 | 24 | 23 | 95.8333 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.1774 | 93.6073 | 92.7515 | 79.6508 | 820 | 56 | 627 | 49 | 48 | 97.9592 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.4314 | 95.4545 | 99.4920 | 57.5943 | 1176 | 56 | 1175 | 6 | 5 | 83.3333 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 60.9324 | 77.3279 | 50.2732 | 71.4953 | 191 | 56 | 184 | 182 | 167 | 91.7582 | |
| gduggal-bwavard | SNP | ti | map_siren | hetalt | 0.0000 | 1.7544 | 0.0000 | 0.0000 | 1 | 56 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 53.8091 | 57.5758 | 50.5051 | 84.7692 | 76 | 56 | 50 | 49 | 21 | 42.8571 | |
| eyeh-varpipe | SNP | tv | map_l100_m1_e0 | * | 97.3811 | 99.7714 | 95.1026 | 69.0013 | 24445 | 56 | 24274 | 1250 | 21 | 1.6800 | |
| eyeh-varpipe | SNP | tv | map_l100_m2_e0 | * | 97.4043 | 99.7763 | 95.1424 | 70.6557 | 24977 | 56 | 24816 | 1267 | 21 | 1.6575 | |
| eyeh-varpipe | SNP | tv | map_l100_m2_e1 | * | 97.4090 | 99.7785 | 95.1495 | 70.7126 | 25227 | 56 | 25050 | 1277 | 21 | 1.6445 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 33.7079 | 21.1268 | 83.3333 | 85.3659 | 15 | 56 | 15 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 51.2821 | 34.8837 | 96.7742 | 79.1946 | 30 | 56 | 30 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | * | func_cds | homalt | 99.5972 | 99.1976 | 100.0000 | 22.2746 | 6923 | 56 | 6923 | 0 | 0 | ||
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 24.4399 | 15.1515 | 63.1579 | 53.6585 | 10 | 56 | 12 | 7 | 7 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 94.6645 | 94.1361 | 95.1988 | 74.6771 | 899 | 56 | 1269 | 64 | 58 | 90.6250 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m2_e1 | * | 96.2343 | 95.9857 | 96.4842 | 82.1695 | 1339 | 56 | 2168 | 79 | 60 | 75.9494 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.6667 | 82.9268 | 100.0000 | 53.4653 | 272 | 56 | 47 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5655 | 97.5492 | 99.6032 | 43.6746 | 2229 | 56 | 2510 | 10 | 3 | 30.0000 | |
| gduggal-bwafb | INDEL | D1_5 | map_l100_m2_e0 | * | 97.6865 | 97.0757 | 98.3051 | 84.3163 | 1859 | 56 | 1856 | 32 | 6 | 18.7500 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.7249 | 90.0709 | 97.6879 | 63.9583 | 508 | 56 | 507 | 12 | 9 | 75.0000 | |
| gduggal-bwafb | INDEL | I6_15 | map_siren | * | 89.4095 | 81.6393 | 98.8142 | 76.5306 | 249 | 56 | 250 | 3 | 3 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7471 | 99.5042 | 99.9911 | 53.7923 | 11240 | 56 | 11209 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l125_m1_e0 | het | 97.3392 | 95.8052 | 98.9231 | 79.2399 | 1279 | 56 | 1286 | 14 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l150_m2_e0 | * | 97.5824 | 96.0227 | 99.1935 | 85.3475 | 1352 | 56 | 1353 | 11 | 1 | 9.0909 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.3412 | 90.9091 | 98.0427 | 61.3214 | 560 | 56 | 551 | 11 | 10 | 90.9091 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m2_e1 | het | 93.9532 | 93.0864 | 94.8363 | 87.4783 | 754 | 56 | 753 | 41 | 29 | 70.7317 | |
| jpowers-varprowl | SNP | tv | HG002complexvar | homalt | 99.4724 | 99.9411 | 99.0081 | 25.6082 | 95055 | 56 | 95130 | 953 | 743 | 77.9643 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m0_e0 | * | 93.8918 | 93.5110 | 94.2757 | 85.2184 | 807 | 56 | 807 | 49 | 23 | 46.9388 | |
| mlin-fermikit | INDEL | * | map_l250_m2_e0 | homalt | 60.5128 | 51.3043 | 73.7500 | 92.2854 | 59 | 56 | 59 | 21 | 20 | 95.2381 | |
| mlin-fermikit | INDEL | * | map_l250_m2_e1 | homalt | 60.9137 | 51.7241 | 74.0741 | 92.4791 | 60 | 56 | 60 | 21 | 20 | 95.2381 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 41.1619 | 58.5185 | 31.7460 | 42.9003 | 79 | 56 | 60 | 129 | 126 | 97.6744 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l100_m1_e0 | * | 98.1106 | 96.9697 | 99.2786 | 76.3393 | 1792 | 56 | 1789 | 13 | 1 | 7.6923 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1175 | 98.9995 | 99.2358 | 63.1487 | 5541 | 56 | 5454 | 42 | 17 | 40.4762 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7965 | 99.5102 | 98.0929 | 39.5838 | 11377 | 56 | 11419 | 222 | 6 | 2.7027 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 79.3651 | 72.8155 | 87.2093 | 85.2991 | 150 | 56 | 150 | 22 | 10 | 45.4545 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 84.7915 | 95.5414 | 76.2159 | 71.9574 | 1200 | 56 | 1426 | 445 | 60 | 13.4831 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.5207 | 98.4691 | 96.5904 | 42.5528 | 3602 | 56 | 6799 | 240 | 41 | 17.0833 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 95.1028 | 94.4279 | 95.7874 | 61.2966 | 949 | 56 | 955 | 42 | 40 | 95.2381 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 86.3984 | 76.3713 | 99.4565 | 26.6932 | 181 | 56 | 183 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 49.0909 | 32.5301 | 100.0000 | 83.3333 | 27 | 56 | 1 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | map_siren | * | 71.0638 | 81.6393 | 62.9139 | 77.5520 | 249 | 56 | 285 | 168 | 8 | 4.7619 | |
| anovak-vg | SNP | ti | func_cds | homalt | 99.1630 | 98.9384 | 99.3887 | 18.9378 | 5219 | 56 | 5203 | 32 | 30 | 93.7500 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | het | 95.1831 | 93.9394 | 96.4602 | 91.7945 | 868 | 56 | 872 | 32 | 4 | 12.5000 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.2973 | 98.6962 | 99.9057 | 48.2245 | 4239 | 56 | 4239 | 4 | 1 | 25.0000 | |