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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22051-22100 / 86044 show all | |||||||||||||||
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 21.4286 | 19.5652 | 23.6842 | 60.8247 | 9 | 37 | 9 | 29 | 29 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | segdup | het | 98.2095 | 97.4761 | 98.9540 | 92.5626 | 1429 | 37 | 1419 | 15 | 2 | 13.3333 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_l150_m2_e1 | het | 96.0425 | 92.9119 | 99.3915 | 79.1102 | 485 | 37 | 490 | 3 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.1564 | 96.8697 | 99.4778 | 38.9804 | 1145 | 37 | 1143 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4763 | 99.0588 | 99.8974 | 52.8829 | 3894 | 37 | 3894 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8615 | 99.7820 | 99.9410 | 72.3104 | 16938 | 37 | 16938 | 10 | 6 | 60.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8615 | 99.7820 | 99.9410 | 72.3104 | 16938 | 37 | 16938 | 10 | 6 | 60.0000 | |
| hfeng-pmm3 | SNP | tv | map_l150_m0_e0 | het | 98.8723 | 98.6986 | 99.0466 | 80.7883 | 2806 | 37 | 2805 | 27 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3560 | 99.6428 | 97.1020 | 45.5337 | 10320 | 37 | 10320 | 308 | 303 | 98.3766 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.4677 | 94.4444 | 96.5135 | 88.1879 | 629 | 37 | 609 | 22 | 5 | 22.7273 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 93.9867 | 89.1496 | 99.3789 | 58.6118 | 304 | 37 | 320 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.0043 | 94.4361 | 89.6947 | 85.2186 | 628 | 37 | 470 | 54 | 47 | 87.0370 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l100_m2_e0 | het | 98.1096 | 97.0541 | 99.1883 | 80.7169 | 1219 | 37 | 1222 | 10 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l100_m2_e1 | het | 98.1277 | 97.0820 | 99.1961 | 80.8880 | 1231 | 37 | 1234 | 10 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | HG002compoundhet | het | 85.4445 | 90.8642 | 80.6349 | 57.3748 | 368 | 37 | 254 | 61 | 60 | 98.3607 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0004 | 93.9245 | 96.1014 | 81.4130 | 572 | 37 | 493 | 20 | 18 | 90.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4663 | 97.1991 | 99.7669 | 60.2778 | 1284 | 37 | 1284 | 3 | 1 | 33.3333 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.4677 | 94.4444 | 96.5135 | 88.1879 | 629 | 37 | 609 | 22 | 5 | 22.7273 | |
| jlack-gatk | SNP | ti | segdup | * | 98.4574 | 99.8106 | 97.1403 | 92.8551 | 19500 | 37 | 19498 | 574 | 10 | 1.7422 | |
| jli-custom | INDEL | * | map_l125_m2_e0 | * | 98.5850 | 98.3151 | 98.8564 | 86.6789 | 2159 | 37 | 2161 | 25 | 8 | 32.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9250 | 98.8608 | 89.4585 | 75.5441 | 3211 | 37 | 3106 | 366 | 29 | 7.9235 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 70.2459 | 57.4713 | 90.3226 | 99.9104 | 50 | 37 | 56 | 6 | 3 | 50.0000 | |
| eyeh-varpipe | INDEL | I6_15 | map_l100_m2_e0 | * | 76.3242 | 68.1034 | 86.8020 | 75.9463 | 79 | 37 | 171 | 26 | 24 | 92.3077 | |
| eyeh-varpipe | INDEL | I6_15 | map_l100_m2_e1 | * | 76.1809 | 68.1034 | 86.4322 | 76.0241 | 79 | 37 | 172 | 27 | 25 | 92.5926 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 27.4510 | 15.9091 | 100.0000 | 99.6394 | 7 | 37 | 7 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | segdup | het | 90.5367 | 97.4761 | 84.5196 | 96.2639 | 1429 | 37 | 1425 | 261 | 213 | 81.6092 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m1_e0 | * | 54.0541 | 57.4713 | 51.0204 | 92.8363 | 50 | 37 | 50 | 48 | 21 | 43.7500 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m2_e0 | * | 55.4705 | 58.8889 | 52.4272 | 93.3117 | 53 | 37 | 54 | 49 | 21 | 42.8571 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 37 | 0 | 0 | 0 | |||
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 37 | 0 | 0 | 0 | |||
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 71.6652 | 92.4180 | 58.5235 | 76.3191 | 451 | 37 | 436 | 309 | 284 | 91.9094 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 72.1859 | 74.1259 | 70.3448 | 95.1146 | 106 | 37 | 102 | 43 | 11 | 25.5814 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.1162 | 97.6582 | 96.5801 | 61.6655 | 1543 | 37 | 1525 | 54 | 6 | 11.1111 | |
| gduggal-bwavard | SNP | ti | map_l250_m0_e0 | het | 82.1372 | 96.0385 | 71.7514 | 95.4014 | 897 | 37 | 889 | 350 | 7 | 2.0000 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.8110 | 97.2305 | 94.4322 | 69.1595 | 1299 | 37 | 1289 | 76 | 8 | 10.5263 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | hetalt | 89.7041 | 82.1256 | 98.8235 | 43.1438 | 170 | 37 | 168 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | func_cds | homalt | 99.6481 | 99.2986 | 100.0000 | 20.6003 | 5238 | 37 | 5238 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.3524 | 95.1444 | 95.5614 | 69.5669 | 725 | 37 | 732 | 34 | 14 | 41.1765 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.3146 | 95.6573 | 99.0303 | 86.2431 | 815 | 37 | 817 | 8 | 8 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0761 | 97.2854 | 98.8798 | 74.4855 | 1326 | 37 | 1324 | 15 | 8 | 53.3333 | |
| ndellapenna-hhga | INDEL | I6_15 | HG002complexvar | homalt | 96.3193 | 96.9522 | 95.6946 | 54.2209 | 1177 | 37 | 1178 | 53 | 36 | 67.9245 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5327 | 99.1984 | 99.8692 | 31.8675 | 4579 | 37 | 4580 | 6 | 1 | 16.6667 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 65.2182 | 88.7879 | 51.5371 | 58.1061 | 293 | 37 | 285 | 268 | 261 | 97.3881 | |
| mlin-fermikit | INDEL | D6_15 | map_l125_m1_e0 | * | 74.9115 | 68.3761 | 82.8283 | 83.9286 | 80 | 37 | 82 | 17 | 11 | 64.7059 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.9790 | 96.8591 | 87.5672 | 69.0278 | 1141 | 37 | 1141 | 162 | 155 | 95.6790 | |
| mlin-fermikit | INDEL | I6_15 | map_l100_m1_e0 | * | 76.2909 | 67.5439 | 87.6404 | 81.8367 | 77 | 37 | 78 | 11 | 10 | 90.9091 | |
| mlin-fermikit | INDEL | I6_15 | map_l100_m2_e0 | * | 76.7503 | 68.1034 | 87.9121 | 83.6036 | 79 | 37 | 80 | 11 | 10 | 90.9091 | |
| mlin-fermikit | INDEL | I6_15 | map_l100_m2_e1 | * | 76.7503 | 68.1034 | 87.9121 | 83.9789 | 79 | 37 | 80 | 11 | 10 | 90.9091 | |
| mlin-fermikit | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.9682 | 99.6336 | 96.3576 | 67.1524 | 10060 | 37 | 10079 | 381 | 340 | 89.2388 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.9203 | 85.7143 | 99.0950 | 48.1221 | 222 | 37 | 219 | 2 | 2 | 100.0000 | |