PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78401-78450 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.3420 | 79.4704 | 92.1504 | 48.6116 | 2551 | 659 | 2524 | 215 | 182 | 84.6512 | |
| ckim-isaac | INDEL | I16_PLUS | * | het | 78.5832 | 69.8308 | 89.8441 | 60.3038 | 1898 | 820 | 1902 | 215 | 129 | 60.0000 | |
| gduggal-snapplat | SNP | * | segdup | * | 98.9750 | 98.7209 | 99.2304 | 93.4858 | 27708 | 359 | 27723 | 215 | 30 | 13.9535 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e0 | het | 91.5991 | 98.9650 | 85.2538 | 88.9688 | 1243 | 13 | 1243 | 215 | 63 | 29.3023 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 83.5587 | 94.3683 | 74.9709 | 75.2021 | 620 | 37 | 644 | 215 | 21 | 9.7674 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 22.9391 | 31.0680 | 18.1818 | 56.7921 | 64 | 142 | 48 | 216 | 4 | 1.8519 | |
| ghariani-varprowl | INDEL | I1_5 | map_siren | het | 93.1801 | 98.4533 | 88.4430 | 87.0613 | 1655 | 26 | 1653 | 216 | 106 | 49.0741 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 74.5401 | 60.5690 | 96.8890 | 74.8497 | 6728 | 4380 | 6727 | 216 | 42 | 19.4444 | |
| gduggal-bwaplat | INDEL | D1_5 | * | hetalt | 83.8440 | 73.7042 | 97.2186 | 75.9425 | 7551 | 2694 | 7550 | 216 | 214 | 99.0741 | |
| qzeng-custom | INDEL | D16_PLUS | map_l100_m2_e1 | * | 36.6856 | 81.4433 | 23.6749 | 89.0986 | 79 | 18 | 67 | 216 | 1 | 0.4630 | |
| qzeng-custom | INDEL | D1_5 | HG002complexvar | het | 98.6823 | 98.3530 | 99.0138 | 55.4973 | 20423 | 342 | 21686 | 216 | 103 | 47.6852 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.1236 | 82.5688 | 83.6858 | 64.5989 | 360 | 76 | 1108 | 216 | 72 | 33.3333 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002compoundhet | homalt | 18.1818 | 100.0000 | 10.0000 | 54.4592 | 24 | 0 | 24 | 216 | 151 | 69.9074 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.2568 | 87.6742 | 84.8845 | 71.5339 | 1195 | 168 | 1213 | 216 | 204 | 94.4444 | |
| jli-custom | INDEL | I6_15 | HG002compoundhet | * | 95.9804 | 94.5419 | 97.4633 | 35.3700 | 8297 | 479 | 8299 | 216 | 208 | 96.2963 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 45.4140 | 30.7174 | 87.0736 | 43.4900 | 1460 | 3293 | 1455 | 216 | 197 | 91.2037 | |
| cchapple-custom | INDEL | I6_15 | * | homalt | 98.0872 | 99.5993 | 96.6202 | 48.7819 | 6214 | 25 | 6175 | 216 | 214 | 99.0741 | |
| ckim-vqsr | SNP | * | map_l150_m2_e1 | * | 66.6447 | 50.3105 | 98.6844 | 91.5888 | 16205 | 16005 | 16202 | 216 | 3 | 1.3889 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1088 | 97.1353 | 99.1021 | 39.2213 | 23837 | 703 | 23839 | 216 | 207 | 95.8333 | |
| anovak-vg | INDEL | D16_PLUS | HG002compoundhet | homalt | 22.5256 | 75.0000 | 13.2530 | 46.6809 | 6 | 2 | 33 | 216 | 158 | 73.1481 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 52.6463 | 45.0798 | 63.2653 | 66.5529 | 339 | 413 | 372 | 216 | 150 | 69.4444 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.1189 | 91.5878 | 81.2663 | 80.6056 | 871 | 80 | 937 | 216 | 179 | 82.8704 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | het | 99.0798 | 99.3430 | 98.8180 | 74.4018 | 18146 | 120 | 18142 | 217 | 33 | 15.2074 | |
| jli-custom | INDEL | D6_15 | * | * | 98.6381 | 98.1220 | 99.1595 | 51.2932 | 25602 | 490 | 25602 | 217 | 202 | 93.0876 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.8814 | 39.9386 | 78.2347 | 54.0553 | 780 | 1173 | 780 | 217 | 203 | 93.5484 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 86.7364 | 78.3970 | 97.0612 | 92.7953 | 7160 | 1973 | 7167 | 217 | 34 | 15.6682 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 86.7364 | 78.3970 | 97.0612 | 92.7953 | 7160 | 1973 | 7167 | 217 | 34 | 15.6682 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 80.5920 | 93.3333 | 70.9115 | 86.5051 | 672 | 48 | 529 | 217 | 24 | 11.0599 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 60.5212 | 53.0761 | 70.3956 | 56.0815 | 509 | 450 | 516 | 217 | 206 | 94.9309 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 0.0000 | 0.0000 | 21.0909 | 34.8341 | 0 | 1 | 58 | 217 | 181 | 83.4101 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2538 | 97.1415 | 99.3919 | 50.2946 | 35546 | 1046 | 35469 | 217 | 179 | 82.4885 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9892 | 98.4640 | 99.5201 | 68.3963 | 45000 | 702 | 45000 | 217 | 24 | 11.0599 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9892 | 98.4640 | 99.5201 | 68.3963 | 45000 | 702 | 45000 | 217 | 24 | 11.0599 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.8178 | 81.4097 | 92.9955 | 56.2615 | 2899 | 662 | 2881 | 217 | 142 | 65.4378 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.4728 | 95.2120 | 95.7351 | 40.3377 | 4872 | 245 | 4871 | 217 | 88 | 40.5530 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 87.4099 | 82.2078 | 93.3149 | 53.2942 | 3031 | 656 | 3043 | 218 | 199 | 91.2844 | |
| dgrover-gatk | SNP | * | map_l125_m0_e0 | * | 98.9327 | 98.9889 | 98.8765 | 77.4655 | 19189 | 196 | 19186 | 218 | 48 | 22.0183 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.8065 | 98.5086 | 99.1063 | 41.3831 | 24174 | 366 | 24176 | 218 | 209 | 95.8716 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.8698 | 91.3024 | 96.5857 | 72.7788 | 6078 | 579 | 6167 | 218 | 97 | 44.4954 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.8607 | 93.0351 | 96.7593 | 72.4507 | 5677 | 425 | 6509 | 218 | 163 | 74.7706 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.0177 | 97.5624 | 88.8776 | 88.4848 | 1721 | 43 | 1742 | 218 | 16 | 7.3395 | |
| ltrigg-rtg2 | SNP | ti | HG002complexvar | * | 99.8779 | 99.7988 | 99.9570 | 17.4272 | 507413 | 1023 | 507316 | 218 | 98 | 44.9541 | |
| cchapple-custom | SNP | tv | HG002complexvar | * | 99.7805 | 99.6506 | 99.9108 | 21.2813 | 245292 | 860 | 244113 | 218 | 153 | 70.1835 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m1_e0 | * | 58.9106 | 52.7711 | 66.6667 | 88.0351 | 438 | 392 | 436 | 218 | 187 | 85.7798 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 19.2271 | 11.7330 | 53.2189 | 75.6912 | 283 | 2129 | 248 | 218 | 182 | 83.4862 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0329 | 91.8045 | 94.2947 | 54.2066 | 3607 | 322 | 3603 | 218 | 214 | 98.1651 | |
| ckim-dragen | SNP | ti | map_l150_m0_e0 | het | 96.9562 | 98.1165 | 95.8230 | 83.8541 | 5001 | 96 | 5001 | 218 | 18 | 8.2569 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 88.0685 | 85.1768 | 91.1634 | 69.1509 | 2264 | 394 | 2249 | 218 | 103 | 47.2477 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1042 | 96.9367 | 99.3002 | 49.5751 | 31012 | 980 | 30935 | 218 | 193 | 88.5321 | |
| ghariani-varprowl | INDEL | * | map_l100_m0_e0 | * | 90.4000 | 93.9859 | 87.0777 | 93.2660 | 1469 | 94 | 1469 | 218 | 66 | 30.2752 | |