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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
81001-81050 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 76.3516 | 67.9439 | 87.1341 | 64.1684 | 2181 | 1029 | 2262 | 334 | 260 | 77.8443 | |
| ciseli-custom | SNP | tv | HG002compoundhet | het | 56.8474 | 77.9585 | 44.7336 | 53.7648 | 3643 | 1030 | 3678 | 4544 | 89 | 1.9586 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0454 | 96.7804 | 99.3438 | 49.5652 | 30962 | 1030 | 30885 | 204 | 187 | 91.6667 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 78.1416 | 74.7118 | 81.9014 | 40.1032 | 3046 | 1031 | 3041 | 672 | 667 | 99.2560 | |
| jpowers-varprowl | SNP | * | map_l125_m1_e0 | het | 96.6905 | 96.3687 | 97.0145 | 77.6907 | 27361 | 1031 | 27361 | 842 | 242 | 28.7411 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 69.9207 | 56.4189 | 91.9178 | 94.1495 | 1336 | 1032 | 1342 | 118 | 26 | 22.0339 | |
| astatham-gatk | SNP | * | map_l250_m2_e0 | * | 92.6519 | 86.9119 | 99.2038 | 90.7351 | 6853 | 1032 | 6853 | 55 | 19 | 34.5455 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.5812 | 92.6383 | 98.7173 | 34.2439 | 12999 | 1033 | 13853 | 180 | 164 | 91.1111 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 15.2225 | 9.4654 | 38.8554 | 56.6013 | 108 | 1033 | 129 | 203 | 109 | 53.6946 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 41.1230 | 32.4837 | 56.0227 | 78.9373 | 497 | 1033 | 493 | 387 | 383 | 98.9664 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 41.1230 | 32.4837 | 56.0227 | 78.9373 | 497 | 1033 | 493 | 387 | 383 | 98.9664 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 18.3933 | 12.4471 | 35.2174 | 39.3140 | 147 | 1034 | 162 | 298 | 265 | 88.9262 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.7447 | 84.4675 | 83.0341 | 89.9808 | 5623 | 1034 | 5643 | 1153 | 77 | 6.6782 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 80.6495 | 78.6024 | 82.8061 | 85.2794 | 3802 | 1035 | 3848 | 799 | 94 | 11.7647 | |
| anovak-vg | INDEL | * | map_l100_m2_e1 | * | 72.2208 | 72.4441 | 71.9990 | 84.9008 | 2721 | 1035 | 2795 | 1087 | 655 | 60.2576 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 20.0155 | 0.0000 | 0.0000 | 259 | 1035 | 0 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7526 | 96.6010 | 98.9320 | 70.8092 | 29444 | 1036 | 28994 | 313 | 239 | 76.3578 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7526 | 96.6010 | 98.9320 | 70.8092 | 29444 | 1036 | 28994 | 313 | 239 | 76.3578 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.4509 | 70.3322 | 91.2863 | 53.7682 | 2456 | 1036 | 1540 | 147 | 142 | 96.5986 | |
| jpowers-varprowl | SNP | * | map_l150_m1_e0 | * | 97.1070 | 96.6121 | 97.6070 | 79.3678 | 29572 | 1037 | 29572 | 725 | 231 | 31.8621 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | * | 98.7938 | 99.5787 | 98.0211 | 25.3464 | 245118 | 1037 | 245440 | 4955 | 529 | 10.6761 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7473 | 94.3151 | 97.2237 | 42.8173 | 17221 | 1038 | 17930 | 512 | 480 | 93.7500 | |
| ckim-isaac | SNP | tv | map_l250_m2_e0 | het | 63.3205 | 46.4948 | 99.2299 | 92.2101 | 902 | 1038 | 902 | 7 | 1 | 14.2857 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 93.7863 | 0.0000 | 0.0000 | 15667 | 1038 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 93.7863 | 0.0000 | 0.0000 | 15667 | 1038 | 0 | 0 | 0 | ||
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.8510 | 97.6024 | 98.1008 | 61.8066 | 42296 | 1039 | 42098 | 815 | 759 | 93.1288 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 91.7285 | 85.5171 | 98.9129 | 30.0899 | 6135 | 1039 | 6460 | 71 | 61 | 85.9155 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 52.7192 | 50.5474 | 55.0862 | 52.4074 | 1062 | 1039 | 991 | 808 | 803 | 99.3812 | |
| jpowers-varprowl | SNP | * | map_l125_m2_e0 | het | 96.7249 | 96.4527 | 96.9986 | 79.0213 | 28278 | 1040 | 28278 | 875 | 244 | 27.8857 | |
| astatham-gatk | SNP | * | map_l250_m2_e1 | * | 92.6875 | 86.9663 | 99.2144 | 90.7902 | 6946 | 1041 | 6946 | 55 | 19 | 34.5455 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.8601 | 67.5701 | 97.6148 | 72.4420 | 2169 | 1041 | 2169 | 53 | 50 | 94.3396 | |
| qzeng-custom | SNP | tv | map_l100_m0_e0 | homalt | 83.9304 | 72.9329 | 98.8335 | 64.8615 | 2805 | 1041 | 2796 | 33 | 33 | 100.0000 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 78.4461 | 79.6640 | 77.2650 | 73.1213 | 4078 | 1041 | 4068 | 1197 | 480 | 40.1003 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 91.6751 | 85.4753 | 98.8445 | 42.9599 | 6132 | 1042 | 941 | 11 | 11 | 100.0000 | |
| gduggal-bwavard | SNP | * | map_l125_m1_e0 | * | 95.6870 | 97.6989 | 93.7563 | 78.5243 | 44284 | 1043 | 43712 | 2911 | 180 | 6.1834 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 92.6853 | 87.1155 | 99.0159 | 25.1484 | 7052 | 1043 | 7244 | 72 | 68 | 94.4444 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 27.0890 | 20.6844 | 39.2387 | 39.7707 | 272 | 1043 | 268 | 415 | 363 | 87.4699 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7006 | 97.8372 | 99.5793 | 71.1392 | 47227 | 1044 | 47105 | 199 | 54 | 27.1357 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 71.7034 | 76.5182 | 67.4586 | 62.2452 | 3402 | 1044 | 3748 | 1808 | 1171 | 64.7677 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 70.2572 | 87.5000 | 58.6914 | 56.3300 | 7315 | 1045 | 7266 | 5114 | 4566 | 89.2843 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 70.2572 | 87.5000 | 58.6914 | 56.3300 | 7315 | 1045 | 7266 | 5114 | 4566 | 89.2843 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.1010 | 77.3614 | 97.0668 | 59.1479 | 3571 | 1045 | 3574 | 108 | 9 | 8.3333 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | hetalt | 66.4170 | 50.0717 | 98.6059 | 45.0179 | 1048 | 1045 | 1061 | 15 | 14 | 93.3333 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.4762 | 95.2989 | 97.6829 | 51.6687 | 21204 | 1046 | 21205 | 503 | 474 | 94.2346 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 73.1048 | 71.1289 | 75.1936 | 73.0650 | 2577 | 1046 | 2622 | 865 | 237 | 27.3988 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e1 | * | 79.8823 | 72.1512 | 89.4689 | 91.7596 | 2710 | 1046 | 2948 | 347 | 39 | 11.2392 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2538 | 97.1415 | 99.3919 | 50.2946 | 35546 | 1046 | 35469 | 217 | 179 | 82.4885 | |
| ckim-isaac | SNP | tv | map_l250_m2_e1 | het | 63.5294 | 46.7176 | 99.2432 | 92.2217 | 918 | 1047 | 918 | 7 | 1 | 14.2857 | |