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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66201-66250 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.0245 | 92.0752 | 98.1691 | 77.4877 | 1127 | 97 | 1126 | 21 | 11 | 52.3810 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.7832 | 94.0810 | 99.6452 | 50.9082 | 5897 | 371 | 5898 | 21 | 4 | 19.0476 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.5046 | 93.7269 | 99.4518 | 53.6591 | 3810 | 255 | 3810 | 21 | 4 | 19.0476 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 0.0000 | 0.0000 | 77.1739 | 94.4910 | 0 | 0 | 71 | 21 | 9 | 42.8571 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 0.0000 | 0.0000 | 77.1739 | 94.4910 | 0 | 0 | 71 | 21 | 9 | 42.8571 | |
| gduggal-snapfb | INDEL | I1_5 | map_l150_m2_e1 | het | 93.8879 | 94.3218 | 93.4579 | 89.6652 | 299 | 18 | 300 | 21 | 3 | 14.2857 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.3092 | 94.0011 | 98.7334 | 63.5924 | 1661 | 106 | 1637 | 21 | 7 | 33.3333 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 39.6010 | 27.0677 | 73.7500 | 90.5101 | 72 | 194 | 59 | 21 | 4 | 19.0476 | |
| gduggal-snapplat | INDEL | D6_15 | map_siren | * | 43.1110 | 29.0766 | 83.3333 | 91.7593 | 148 | 361 | 105 | 21 | 3 | 14.2857 | |
| gduggal-snapfb | SNP | ti | map_l125_m0_e0 | homalt | 96.3354 | 93.3645 | 99.5017 | 80.4209 | 4193 | 298 | 4193 | 21 | 10 | 47.6190 | |
| gduggal-snapvard | INDEL | D6_15 | map_l125_m0_e0 | * | 74.1899 | 72.3404 | 76.1364 | 88.0759 | 34 | 13 | 67 | 21 | 11 | 52.3810 | |
| gduggal-snapvard | INDEL | D6_15 | map_l125_m0_e0 | het | 77.8088 | 82.7586 | 73.4177 | 88.3136 | 24 | 5 | 58 | 21 | 11 | 52.3810 | |
| gduggal-snapvard | SNP | * | map_l150_m0_e0 | homalt | 96.6127 | 93.9349 | 99.4477 | 77.1281 | 3841 | 248 | 3781 | 21 | 16 | 76.1905 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.9292 | 85.2071 | 95.2055 | 89.4101 | 432 | 75 | 417 | 21 | 10 | 47.6190 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8817 | 99.8462 | 99.9171 | 55.0271 | 25320 | 39 | 25323 | 21 | 16 | 76.1905 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.1238 | 98.4538 | 99.8029 | 79.4946 | 10634 | 167 | 10634 | 21 | 12 | 57.1429 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2005 | 98.5314 | 99.8788 | 66.3539 | 17310 | 258 | 17301 | 21 | 11 | 52.3810 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.8761 | 98.7371 | 99.0155 | 76.7875 | 2111 | 27 | 2112 | 21 | 2 | 9.5238 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e0 | het | 77.7080 | 80.2817 | 75.2941 | 89.6341 | 57 | 14 | 64 | 21 | 11 | 52.3810 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e1 | het | 78.0093 | 80.2817 | 75.8621 | 89.5558 | 57 | 14 | 66 | 21 | 11 | 52.3810 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 26.2295 | 25.0000 | 27.5862 | 55.3846 | 6 | 18 | 8 | 21 | 14 | 66.6667 | |
| anovak-vg | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6861 | 95.4198 | 95.9538 | 64.2562 | 500 | 24 | 498 | 21 | 15 | 71.4286 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.7533 | 97.8118 | 97.6948 | 70.8013 | 894 | 20 | 890 | 21 | 8 | 38.0952 | |
| anovak-vg | SNP | tv | map_l100_m0_e0 | homalt | 87.5215 | 78.2371 | 99.3060 | 64.7976 | 3009 | 837 | 3005 | 21 | 17 | 80.9524 | |
| astatham-gatk | INDEL | * | map_l150_m0_e0 | * | 96.2251 | 96.4981 | 95.9538 | 92.9541 | 496 | 18 | 498 | 21 | 4 | 19.0476 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.8600 | 99.6324 | 98.0995 | 67.6806 | 1084 | 4 | 1084 | 21 | 19 | 90.4762 | |
| astatham-gatk | INDEL | D1_5 | HG002complexvar | het | 99.6863 | 99.4751 | 99.8985 | 56.1634 | 20656 | 109 | 20662 | 21 | 12 | 57.1429 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.5536 | 96.0864 | 97.0255 | 75.2541 | 712 | 29 | 685 | 21 | 18 | 85.7143 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m1_e0 | het | 95.4352 | 95.2282 | 95.6432 | 90.0310 | 459 | 23 | 461 | 21 | 3 | 14.2857 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m2_e0 | het | 95.4137 | 94.9416 | 95.8904 | 90.4629 | 488 | 26 | 490 | 21 | 3 | 14.2857 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m2_e1 | het | 95.2826 | 94.6360 | 95.9381 | 90.5225 | 494 | 28 | 496 | 21 | 3 | 14.2857 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5326 | 98.2332 | 92.9766 | 69.5519 | 278 | 5 | 278 | 21 | 21 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 94.3857 | 90.2532 | 98.9147 | 46.6501 | 1889 | 204 | 1914 | 21 | 21 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 91.2060 | 85.1382 | 98.2051 | 87.1018 | 1140 | 199 | 1149 | 21 | 4 | 19.0476 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e0 | * | 91.2346 | 85.1608 | 98.2412 | 87.9589 | 1165 | 203 | 1173 | 21 | 4 | 19.0476 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e1 | * | 91.2086 | 85.0896 | 98.2759 | 87.9905 | 1187 | 208 | 1197 | 21 | 4 | 19.0476 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.8792 | 96.0199 | 97.7540 | 64.3266 | 579 | 24 | 914 | 21 | 15 | 71.4286 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.2022 | 98.8423 | 99.5649 | 69.6516 | 4781 | 56 | 4805 | 21 | 9 | 42.8571 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5129 | 95.5131 | 99.5982 | 26.1932 | 5194 | 244 | 5206 | 21 | 21 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | HG002compoundhet | * | 99.8512 | 99.8226 | 99.8798 | 35.5355 | 17447 | 31 | 17445 | 21 | 14 | 66.6667 | |
| bgallagher-sentieon | SNP | tv | HG002compoundhet | het | 99.6043 | 99.6576 | 99.5511 | 55.0192 | 4657 | 16 | 4657 | 21 | 5 | 23.8095 | |
| rpoplin-dv42 | SNP | * | map_l125_m0_e0 | homalt | 99.0933 | 98.5101 | 99.6834 | 69.3810 | 6612 | 100 | 6612 | 21 | 20 | 95.2381 | |
| rpoplin-dv42 | SNP | ti | HG002compoundhet | homalt | 99.7770 | 99.8377 | 99.7163 | 30.8389 | 7382 | 12 | 7382 | 21 | 20 | 95.2381 | |
| rpoplin-dv42 | SNP | ti | map_l250_m0_e0 | het | 97.5322 | 97.3233 | 97.7419 | 92.5223 | 909 | 25 | 909 | 21 | 11 | 52.3810 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3392 | 99.0283 | 99.6520 | 55.6062 | 6013 | 59 | 6013 | 21 | 19 | 90.4762 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 88.2174 | 92.0732 | 84.6715 | 84.6413 | 151 | 13 | 116 | 21 | 19 | 90.4762 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.0420 | 91.4155 | 98.9681 | 33.4097 | 2002 | 188 | 2014 | 21 | 20 | 95.2381 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.0938 | 92.8279 | 95.3947 | 79.6156 | 453 | 35 | 435 | 21 | 12 | 57.1429 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.0960 | 89.8927 | 98.7117 | 42.9671 | 1592 | 179 | 1609 | 21 | 20 | 95.2381 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 91.5332 | 92.5926 | 90.4977 | 62.7319 | 200 | 16 | 200 | 21 | 15 | 71.4286 | |