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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75701-75750 / 86044 show all | |||||||||||||||
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 68.7241 | 97.0414 | 53.2000 | 69.5122 | 164 | 5 | 133 | 117 | 117 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002complexvar | * | 99.3509 | 99.0558 | 99.6477 | 56.5141 | 33048 | 315 | 33091 | 117 | 105 | 89.7436 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.1088 | 95.8830 | 98.3664 | 54.5270 | 7080 | 304 | 7045 | 117 | 113 | 96.5812 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 87.5446 | 82.8245 | 92.8353 | 37.8851 | 3337 | 692 | 1516 | 117 | 56 | 47.8632 | |
| ghariani-varprowl | SNP | tv | map_siren | homalt | 99.3038 | 99.2865 | 99.3211 | 57.8404 | 17117 | 123 | 17117 | 117 | 71 | 60.6838 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 25.4980 | 31.3725 | 21.4765 | 98.0147 | 32 | 70 | 32 | 117 | 5 | 4.2735 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 0.8029 | 0.4065 | 32.3699 | 65.8777 | 1 | 245 | 56 | 117 | 46 | 39.3162 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e0 | het | 87.3970 | 98.7055 | 78.4133 | 92.5365 | 305 | 4 | 425 | 117 | 42 | 35.8974 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 0.2898 | 0.1456 | 32.5714 | 65.9533 | 1 | 686 | 57 | 118 | 47 | 39.8305 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e1 | het | 87.4676 | 98.7382 | 78.5064 | 92.5981 | 313 | 4 | 431 | 118 | 43 | 36.4407 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 68.7500 | 83.7563 | 58.3039 | 53.7582 | 165 | 32 | 165 | 118 | 105 | 88.9831 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 72.4442 | 68.0556 | 77.4379 | 54.5217 | 392 | 184 | 405 | 118 | 115 | 97.4576 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8275 | 99.6183 | 86.9034 | 74.4470 | 783 | 3 | 783 | 118 | 3 | 2.5424 | |
| ghariani-varprowl | INDEL | * | map_l125_m0_e0 | * | 91.1268 | 94.8980 | 87.6440 | 95.1166 | 837 | 45 | 837 | 118 | 30 | 25.4237 | |
| gduggal-snapplat | INDEL | D1_5 | segdup | * | 87.1437 | 84.2248 | 90.2721 | 96.4637 | 929 | 174 | 1095 | 118 | 18 | 15.2542 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | * | 99.0452 | 99.1281 | 98.9624 | 78.7121 | 11256 | 99 | 11254 | 118 | 24 | 20.3390 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e1 | * | 99.0574 | 99.1393 | 98.9756 | 78.7166 | 11403 | 99 | 11401 | 118 | 24 | 20.3390 | |
| egarrison-hhga | SNP | * | map_l100_m2_e0 | * | 99.5430 | 99.2483 | 99.8395 | 64.7214 | 73408 | 556 | 73409 | 118 | 50 | 42.3729 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 76.9409 | 66.2700 | 91.7077 | 66.5255 | 1281 | 652 | 1305 | 118 | 98 | 83.0508 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 83.2650 | 74.7927 | 93.9018 | 56.7791 | 1804 | 608 | 1817 | 118 | 62 | 52.5424 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1078 | 92.3077 | 95.9796 | 65.5314 | 2784 | 232 | 2817 | 118 | 7 | 5.9322 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e0 | het | 78.3377 | 64.9794 | 98.6095 | 91.3777 | 8370 | 4511 | 8368 | 118 | 2 | 1.6949 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6403 | 99.3747 | 97.9167 | 72.3397 | 5562 | 35 | 5546 | 118 | 106 | 89.8305 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6856 | 99.9087 | 99.4636 | 76.0319 | 21879 | 20 | 21879 | 118 | 117 | 99.1525 | |
| ckim-vqsr | SNP | * | HG002complexvar | * | 98.7826 | 97.6098 | 99.9840 | 19.7255 | 736350 | 18031 | 736201 | 118 | 58 | 49.1525 | |
| ndellapenna-hhga | INDEL | I6_15 | HG002compoundhet | het | 71.9355 | 85.0962 | 62.3003 | 78.5616 | 177 | 31 | 195 | 118 | 77 | 65.2542 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 61.1726 | 50.2392 | 78.1885 | 71.6457 | 420 | 416 | 423 | 118 | 117 | 99.1525 | |
| mlin-fermikit | SNP | * | HG002compoundhet | het | 92.5921 | 86.9234 | 99.0518 | 44.4618 | 12324 | 1854 | 12327 | 118 | 22 | 18.6441 | |
| mlin-fermikit | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.5257 | 96.6749 | 96.3770 | 70.3153 | 3140 | 108 | 3139 | 118 | 63 | 53.3898 | |
| jmaeng-gatk | INDEL | * | HG002complexvar | homalt | 99.7212 | 99.8779 | 99.5650 | 57.3567 | 26994 | 33 | 27007 | 118 | 111 | 94.0678 | |
| jmaeng-gatk | INDEL | D16_PLUS | * | het | 97.5431 | 99.0503 | 96.0810 | 78.7734 | 3129 | 30 | 2893 | 118 | 85 | 72.0339 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 87.3841 | 93.4028 | 82.0941 | 65.3887 | 538 | 38 | 541 | 118 | 116 | 98.3051 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 31.2083 | 26.2195 | 38.5417 | 39.6226 | 43 | 121 | 74 | 118 | 98 | 83.0508 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 76.2575 | 0 | 0 | 0 | 118 | 0 | 0.0000 | ||
| hfeng-pmm3 | SNP | * | map_l100_m0_e0 | het | 99.3509 | 99.2596 | 99.4424 | 70.0348 | 21048 | 157 | 21044 | 118 | 11 | 9.3220 | |
| hfeng-pmm1 | SNP | * | map_l125_m0_e0 | * | 99.1962 | 99.0044 | 99.3888 | 74.3664 | 19192 | 193 | 19189 | 118 | 33 | 27.9661 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.5666 | 98.2288 | 91.1677 | 82.1653 | 1331 | 24 | 1218 | 118 | 65 | 55.0847 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 36.7347 | 85.7143 | 23.3766 | 97.5877 | 36 | 6 | 36 | 118 | 1 | 0.8475 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.8346 | 80.5442 | 83.1669 | 54.9775 | 592 | 143 | 583 | 118 | 117 | 99.1525 | |
| rpoplin-dv42 | SNP | tv | map_l125_m1_e0 | * | 99.1341 | 99.0072 | 99.2613 | 68.8884 | 15857 | 159 | 15855 | 118 | 69 | 58.4746 | |
| rpoplin-dv42 | SNP | ti | * | homalt | 99.9800 | 99.9747 | 99.9853 | 16.8487 | 802835 | 203 | 802832 | 118 | 106 | 89.8305 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6970 | 99.9315 | 99.4637 | 76.0277 | 21884 | 15 | 21884 | 118 | 117 | 99.1525 | |
| ckim-gatk | INDEL | I16_PLUS | * | * | 97.3609 | 96.6128 | 98.1207 | 70.7109 | 6161 | 216 | 6161 | 118 | 83 | 70.3390 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.7737 | 95.3383 | 96.2131 | 64.2456 | 1268 | 62 | 2998 | 118 | 110 | 93.2203 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 58.3686 | 63.6364 | 53.9062 | 70.1284 | 133 | 76 | 138 | 118 | 36 | 30.5085 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 72.6669 | 63.6190 | 84.7150 | 61.4963 | 668 | 382 | 654 | 118 | 77 | 65.2542 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 65.3542 | 82.1429 | 54.2636 | 73.2919 | 138 | 30 | 140 | 118 | 84 | 71.1864 | |
| 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 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | het | 93.1246 | 91.6331 | 94.6655 | 81.5482 | 2048 | 187 | 2094 | 118 | 21 | 17.7966 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7039 | 73.7672 | 91.5543 | 53.9843 | 2199 | 782 | 1290 | 119 | 114 | 95.7983 | |