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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54551-54600 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D16_PLUS | map_siren | het | 92.3788 | 96.1538 | 88.8889 | 96.1410 | 75 | 3 | 72 | 9 | 2 | 22.2222 | |
| gduggal-snapfb | INDEL | I1_5 | map_l250_m1_e0 | * | 92.3810 | 91.5094 | 93.2692 | 96.3636 | 97 | 9 | 97 | 7 | 3 | 42.8571 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 92.3815 | 89.1767 | 95.8253 | 57.6036 | 3477 | 422 | 3489 | 152 | 75 | 49.3421 | |
| anovak-vg | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.3819 | 93.7500 | 91.0531 | 69.7462 | 3045 | 203 | 3104 | 305 | 131 | 42.9508 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_siren | * | 92.3827 | 93.7063 | 91.0959 | 92.6633 | 134 | 9 | 133 | 13 | 1 | 7.6923 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.3833 | 95.4225 | 89.5317 | 74.6685 | 813 | 39 | 650 | 76 | 31 | 40.7895 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.3833 | 99.2084 | 86.4368 | 60.3102 | 376 | 3 | 376 | 59 | 59 | 100.0000 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | het | 92.3834 | 87.8381 | 97.4248 | 82.5144 | 40756 | 5643 | 40745 | 1077 | 78 | 7.2423 | |
| jpowers-varprowl | INDEL | * | map_l150_m2_e0 | het | 92.3836 | 93.0464 | 91.7301 | 91.9202 | 843 | 63 | 843 | 76 | 49 | 64.4737 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.3848 | 95.6522 | 89.3333 | 91.3793 | 66 | 3 | 67 | 8 | 4 | 50.0000 | |
| jpowers-varprowl | SNP | ti | HG002compoundhet | homalt | 92.3856 | 99.8107 | 85.9888 | 37.4563 | 7380 | 14 | 7383 | 1203 | 882 | 73.3167 | |
| qzeng-custom | SNP | * | map_siren | * | 92.3867 | 86.6004 | 99.0016 | 63.6130 | 126634 | 19594 | 125047 | 1261 | 903 | 71.6098 | |
| asubramanian-gatk | INDEL | I6_15 | map_l100_m2_e1 | het | 92.3908 | 88.5246 | 96.6102 | 90.6051 | 54 | 7 | 57 | 2 | 1 | 50.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 92.3921 | 86.0531 | 99.7392 | 40.4272 | 1524 | 247 | 1530 | 4 | 4 | 100.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e0 | * | 92.3931 | 86.6065 | 99.0083 | 90.6397 | 2496 | 386 | 2496 | 25 | 7 | 28.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.3933 | 85.9532 | 99.8765 | 41.6427 | 771 | 126 | 809 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 92.3938 | 89.4378 | 95.5519 | 45.2869 | 12329 | 1456 | 13383 | 623 | 612 | 98.2343 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3955 | 88.2236 | 96.9815 | 64.0909 | 884 | 118 | 996 | 31 | 27 | 87.0968 | |
| jlack-gatk | SNP | tv | map_l150_m0_e0 | * | 92.3966 | 97.9875 | 87.4091 | 87.6580 | 4090 | 84 | 4089 | 589 | 40 | 6.7912 | |
| jpowers-varprowl | SNP | tv | map_l250_m1_e0 | het | 92.3970 | 93.5087 | 91.3115 | 92.1131 | 1671 | 116 | 1671 | 159 | 31 | 19.4969 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e1 | homalt | 92.3972 | 86.9509 | 98.5714 | 81.2719 | 673 | 101 | 897 | 13 | 11 | 84.6154 | |
| gduggal-snapvard | INDEL | * | map_l125_m1_e0 | homalt | 92.3976 | 87.0219 | 98.4813 | 80.4522 | 637 | 95 | 843 | 13 | 11 | 84.6154 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.3980 | 87.5241 | 97.8468 | 61.7037 | 5458 | 778 | 5635 | 124 | 11 | 8.8710 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.3981 | 88.0952 | 97.1429 | 87.9310 | 37 | 5 | 34 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3988 | 87.3134 | 98.1132 | 62.3817 | 468 | 68 | 468 | 9 | 7 | 77.7778 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.3991 | 97.0540 | 88.1703 | 71.9469 | 593 | 18 | 559 | 75 | 71 | 94.6667 | |
| gduggal-bwavard | INDEL | * | func_cds | * | 92.3991 | 93.2584 | 91.5556 | 46.3647 | 415 | 30 | 412 | 38 | 24 | 63.1579 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 92.3995 | 86.2069 | 99.5506 | 43.8131 | 975 | 156 | 443 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | map_l125_m0_e0 | * | 92.4000 | 89.3617 | 95.6522 | 92.1098 | 42 | 5 | 44 | 2 | 1 | 50.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.4011 | 86.1348 | 99.6507 | 30.4797 | 1112 | 179 | 1141 | 4 | 4 | 100.0000 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | * | 92.4051 | 96.3396 | 88.7794 | 82.5294 | 31031 | 1179 | 30628 | 3871 | 287 | 7.4141 | |
| hfeng-pmm1 | INDEL | * | map_l250_m0_e0 | * | 92.4051 | 93.5897 | 91.2500 | 97.0717 | 73 | 5 | 73 | 7 | 2 | 28.5714 | |
| jli-custom | INDEL | * | map_l250_m0_e0 | * | 92.4051 | 93.5897 | 91.2500 | 97.4416 | 73 | 5 | 73 | 7 | 2 | 28.5714 | |
| raldana-dualsentieon | INDEL | I16_PLUS | HG002compoundhet | * | 92.4081 | 89.1741 | 95.8856 | 50.9476 | 1911 | 232 | 1911 | 82 | 81 | 98.7805 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 92.4081 | 90.2665 | 94.6537 | 88.7322 | 779 | 84 | 779 | 44 | 5 | 11.3636 | |
| mlin-fermikit | INDEL | D6_15 | HG002complexvar | het | 92.4085 | 90.4808 | 94.4202 | 55.5173 | 2823 | 297 | 2809 | 166 | 152 | 91.5663 | |
| gduggal-snapfb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.4085 | 98.5294 | 87.0036 | 79.8311 | 1206 | 18 | 1205 | 180 | 12 | 6.6667 | |
| astatham-gatk | SNP | tv | map_l250_m2_e1 | * | 92.4090 | 86.6255 | 99.0200 | 90.7000 | 2526 | 390 | 2526 | 25 | 7 | 28.0000 | |
| gduggal-snapvard | INDEL | * | map_l150_m1_e0 | homalt | 92.4102 | 87.0130 | 98.5213 | 84.2778 | 402 | 60 | 533 | 8 | 6 | 75.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.4122 | 85.8946 | 100.0000 | 32.3455 | 1565 | 257 | 1598 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D6_15 | * | het | 92.4134 | 97.5414 | 87.7976 | 56.6240 | 11307 | 285 | 12059 | 1676 | 1576 | 94.0334 | |
| mlin-fermikit | SNP | * | tech_badpromoters | het | 92.4138 | 87.0130 | 98.5294 | 38.1818 | 67 | 10 | 67 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.4148 | 85.9485 | 99.9334 | 29.8926 | 1468 | 240 | 1500 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | * | map_l150_m2_e1 | * | 92.4162 | 91.0354 | 93.8395 | 90.8085 | 1310 | 129 | 1310 | 86 | 55 | 63.9535 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 92.4174 | 87.2960 | 98.1771 | 57.2145 | 749 | 109 | 754 | 14 | 4 | 28.5714 | |
| rpoplin-dv42 | INDEL | I6_15 | map_siren | het | 92.4188 | 89.5105 | 95.5224 | 83.4568 | 128 | 15 | 128 | 6 | 6 | 100.0000 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e0 | homalt | 92.4285 | 87.0249 | 98.5475 | 81.2093 | 664 | 99 | 882 | 13 | 11 | 84.6154 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 92.4298 | 90.2778 | 94.6869 | 59.3991 | 520 | 56 | 499 | 28 | 9 | 32.1429 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 92.4301 | 93.6681 | 91.2243 | 68.7320 | 1287 | 87 | 1289 | 124 | 91 | 73.3871 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | * | 92.4318 | 96.0278 | 89.0953 | 81.2252 | 18929 | 783 | 18751 | 2295 | 187 | 8.1482 | |