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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82001-82050 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | D16_PLUS | HG002complexvar | * | 75.2016 | 72.3676 | 78.2666 | 64.6225 | 1189 | 454 | 1192 | 331 | 268 | 80.9668 | |
| ndellapenna-hhga | SNP | * | HG002complexvar | homalt | 99.8626 | 99.8292 | 99.8960 | 19.9404 | 288081 | 493 | 288110 | 300 | 268 | 89.3333 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | het | 86.9738 | 82.7064 | 91.7055 | 77.8323 | 3386 | 708 | 3151 | 285 | 268 | 94.0351 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 82.8791 | 91.0940 | 76.0233 | 83.7724 | 26154 | 2557 | 25854 | 8154 | 268 | 3.2867 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 82.8791 | 91.0940 | 76.0233 | 83.7724 | 26154 | 2557 | 25854 | 8154 | 268 | 3.2867 | |
| rpoplin-dv42 | SNP | * | * | het | 99.9475 | 99.9278 | 99.9673 | 19.5765 | 1872234 | 1353 | 1872094 | 613 | 268 | 43.7194 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2915 | 95.8966 | 98.7276 | 50.7699 | 21337 | 913 | 21338 | 275 | 268 | 97.4545 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 79.1116 | 70.1992 | 90.6162 | 65.8002 | 2855 | 1212 | 2897 | 300 | 268 | 89.3333 | |
| dgrover-gatk | INDEL | I6_15 | HG002compoundhet | homalt | 18.7311 | 100.0000 | 10.3333 | 64.1577 | 31 | 0 | 31 | 269 | 268 | 99.6283 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 84.8964 | 75.6945 | 96.6451 | 41.6459 | 7929 | 2546 | 7922 | 275 | 269 | 97.8182 | |
| gduggal-bwavard | SNP | * | * | homalt | 99.5128 | 99.0597 | 99.9700 | 16.7717 | 1169065 | 11097 | 1159771 | 348 | 269 | 77.2989 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 33.9034 | 47.8673 | 26.2467 | 55.9028 | 101 | 110 | 100 | 281 | 269 | 95.7295 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.3000 | 98.0590 | 92.6920 | 44.9432 | 3587 | 71 | 3729 | 294 | 269 | 91.4966 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 70.2479 | 94.7075 | 55.8292 | 51.1236 | 340 | 19 | 340 | 269 | 269 | 100.0000 | |
| gduggal-snapvard | INDEL | D1_5 | map_siren | * | 89.9255 | 93.9643 | 86.2197 | 83.0558 | 3316 | 213 | 3729 | 596 | 269 | 45.1342 | |
| gduggal-snapvard | SNP | * | HG002complexvar | homalt | 98.1658 | 96.5628 | 99.8230 | 18.7873 | 278656 | 9919 | 269038 | 477 | 269 | 56.3941 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e0 | * | 85.9487 | 92.0310 | 80.6206 | 88.8530 | 2021 | 175 | 2754 | 662 | 269 | 40.6344 | |
| gduggal-snapfb | SNP | ti | * | homalt | 99.7832 | 99.8062 | 99.7602 | 19.1162 | 801483 | 1556 | 801532 | 1927 | 269 | 13.9595 | |
| gduggal-snapfb | SNP | * | map_l150_m0_e0 | * | 94.8356 | 94.4731 | 95.2010 | 82.0124 | 11367 | 665 | 11367 | 573 | 270 | 47.1204 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 36.3779 | 31.5041 | 43.0357 | 63.8943 | 155 | 337 | 241 | 319 | 270 | 84.6395 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e1 | * | 85.9747 | 92.0000 | 80.6901 | 88.9628 | 2047 | 178 | 2783 | 666 | 270 | 40.5405 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 42.0233 | 85.0394 | 27.9070 | 48.4000 | 108 | 19 | 108 | 279 | 270 | 96.7742 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 58.1410 | 81.6327 | 45.1485 | 57.8816 | 400 | 90 | 228 | 277 | 270 | 97.4729 | |
| cchapple-custom | SNP | ti | map_l100_m1_e0 | * | 97.7073 | 97.6424 | 97.7722 | 66.9622 | 46801 | 1130 | 46783 | 1066 | 270 | 25.3283 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5115 | 98.1663 | 98.8593 | 41.0712 | 24090 | 450 | 24092 | 278 | 270 | 97.1223 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7746 | 96.6611 | 98.9141 | 61.8918 | 63169 | 2182 | 63489 | 697 | 270 | 38.7374 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7746 | 96.6611 | 98.9141 | 61.8918 | 63169 | 2182 | 63489 | 697 | 270 | 38.7374 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7839 | 96.9412 | 98.6414 | 47.7167 | 19966 | 630 | 19967 | 275 | 271 | 98.5455 | |
| gduggal-snapplat | SNP | tv | map_l100_m0_e0 | het | 92.3125 | 91.6921 | 92.9413 | 85.1008 | 6622 | 600 | 6623 | 503 | 271 | 53.8767 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 55.0999 | 88.5135 | 40.0000 | 49.5006 | 131 | 17 | 182 | 273 | 271 | 99.2674 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.5231 | 92.2277 | 96.9357 | 58.1370 | 3726 | 314 | 10281 | 325 | 271 | 83.3846 | |
| qzeng-custom | SNP | tv | map_l125_m1_e0 | * | 84.7104 | 74.9376 | 97.4144 | 82.6672 | 12002 | 4014 | 11981 | 318 | 271 | 85.2201 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 48.8684 | 40.9881 | 60.5000 | 69.8341 | 755 | 1087 | 726 | 474 | 272 | 57.3840 | |
| ckim-gatk | INDEL | I6_15 | HG002compoundhet | homalt | 18.5075 | 100.0000 | 10.1974 | 63.1068 | 31 | 0 | 31 | 273 | 272 | 99.6337 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 19.5758 | 15.3515 | 27.0073 | 33.7097 | 107 | 590 | 111 | 300 | 272 | 90.6667 | |
| ckim-vqsr | INDEL | I6_15 | HG002compoundhet | homalt | 18.5075 | 100.0000 | 10.1974 | 63.1068 | 31 | 0 | 31 | 273 | 272 | 99.6337 | |
| dgrover-gatk | INDEL | I6_15 | * | homalt | 97.7715 | 99.8557 | 95.7725 | 55.4177 | 6230 | 9 | 6230 | 275 | 272 | 98.9091 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002compoundhet | * | 86.6377 | 85.3054 | 88.0123 | 33.8869 | 1997 | 344 | 1997 | 272 | 272 | 100.0000 | |
| cchapple-custom | SNP | ti | map_l100_m2_e0 | het | 97.1509 | 97.7892 | 96.5210 | 73.0558 | 29945 | 677 | 29963 | 1080 | 273 | 25.2778 | |
| ciseli-custom | SNP | tv | HG002complexvar | het | 94.7007 | 95.5637 | 93.8531 | 24.0959 | 144047 | 6687 | 143323 | 9387 | 273 | 2.9083 | |
| gduggal-snapplat | SNP | * | HG002compoundhet | homalt | 94.8523 | 93.4799 | 96.2656 | 42.1750 | 10079 | 703 | 10002 | 388 | 273 | 70.3608 | |
| ghariani-varprowl | SNP | * | map_l125_m1_e0 | * | 97.9382 | 98.7204 | 97.1684 | 75.3206 | 44747 | 580 | 44747 | 1304 | 273 | 20.9356 | |
| ghariani-varprowl | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.8554 | 99.9208 | 95.8736 | 65.4859 | 10089 | 8 | 10107 | 435 | 273 | 62.7586 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.2241 | 98.9337 | 99.5161 | 74.5848 | 63744 | 687 | 63757 | 310 | 273 | 88.0645 | |
| jpowers-varprowl | INDEL | D16_PLUS | HG002complexvar | * | 75.6960 | 71.3329 | 80.6276 | 65.0203 | 1172 | 471 | 1182 | 284 | 273 | 96.1268 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e1 | * | 75.3445 | 66.1342 | 87.5352 | 80.6829 | 2484 | 1272 | 2486 | 354 | 273 | 77.1186 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.8049 | 97.4163 | 96.2011 | 51.9614 | 10821 | 287 | 18967 | 749 | 273 | 36.4486 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.7617 | 96.8094 | 92.7988 | 67.6203 | 3641 | 120 | 3634 | 282 | 273 | 96.8085 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.7617 | 96.8094 | 92.7988 | 67.6203 | 3641 | 120 | 3634 | 282 | 273 | 96.8085 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4923 | 90.0065 | 83.2423 | 70.9011 | 1387 | 154 | 1371 | 276 | 273 | 98.9130 | |