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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
42701-42750 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 61.2714 | 47.5666 | 86.0697 | 84.3397 | 1036 | 1142 | 1038 | 168 | 41 | 24.4048 | |
| qzeng-custom | INDEL | * | map_l250_m1_e0 | het | 77.2075 | 70.0000 | 86.0697 | 98.2587 | 133 | 57 | 173 | 28 | 15 | 53.5714 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.5672 | 91.1998 | 86.0824 | 76.7383 | 17856 | 1723 | 18339 | 2965 | 857 | 28.9039 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.5672 | 91.1998 | 86.0824 | 76.7383 | 17856 | 1723 | 18339 | 2965 | 857 | 28.9039 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1277 | 99.0847 | 86.0835 | 48.4103 | 433 | 4 | 433 | 70 | 70 | 100.0000 | |
| ghariani-varprowl | INDEL | D1_5 | map_l150_m2_e1 | * | 90.5545 | 95.5013 | 86.0950 | 91.3170 | 743 | 35 | 743 | 120 | 22 | 18.3333 | |
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | * | 76.1289 | 68.2288 | 86.0979 | 58.5597 | 1121 | 522 | 1090 | 176 | 59 | 33.5227 | |
| gduggal-bwavard | SNP | tv | map_l150_m2_e1 | het | 91.8305 | 98.3805 | 86.0982 | 85.8449 | 7229 | 119 | 7209 | 1164 | 45 | 3.8660 | |
| ciseli-custom | SNP | ti | map_l150_m0_e0 | homalt | 84.9597 | 83.8464 | 86.1028 | 73.9645 | 2315 | 446 | 2311 | 373 | 299 | 80.1609 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.0249 | 90.0274 | 86.1096 | 53.5183 | 5263 | 583 | 4761 | 768 | 648 | 84.3750 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.0249 | 90.0274 | 86.1096 | 53.5183 | 5263 | 583 | 4761 | 768 | 648 | 84.3750 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 80.1724 | 75.0000 | 86.1111 | 99.9462 | 93 | 31 | 93 | 15 | 8 | 53.3333 | |
| gduggal-snapplat | INDEL | D6_15 | segdup | * | 57.7618 | 43.4555 | 86.1111 | 95.1968 | 83 | 108 | 62 | 10 | 1 | 10.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.4073 | 86.7056 | 86.1111 | 74.4351 | 1337 | 205 | 1364 | 220 | 118 | 53.6364 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m2_e0 | het | 89.8551 | 93.9394 | 86.1111 | 97.9417 | 62 | 4 | 62 | 10 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m2_e1 | het | 89.8551 | 93.9394 | 86.1111 | 98.0083 | 62 | 4 | 62 | 10 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | ti | map_l250_m2_e0 | * | 91.4486 | 97.4840 | 86.1170 | 92.1941 | 4882 | 126 | 4857 | 783 | 27 | 3.4483 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.0881 | 92.2652 | 86.1224 | 81.9720 | 334 | 28 | 211 | 34 | 34 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 91.2274 | 96.9697 | 86.1272 | 74.9275 | 448 | 14 | 447 | 72 | 72 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m0_e0 | * | 62.6026 | 49.1713 | 86.1290 | 76.1722 | 267 | 276 | 267 | 43 | 36 | 83.7209 | |
| mlin-fermikit | INDEL | I6_15 | map_siren | het | 82.8019 | 79.7203 | 86.1314 | 81.4363 | 114 | 29 | 118 | 19 | 17 | 89.4737 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.2444 | 82.4369 | 86.1329 | 57.6838 | 1732 | 369 | 1646 | 265 | 260 | 98.1132 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.2220 | 86.2903 | 86.1538 | 93.2079 | 107 | 17 | 112 | 18 | 1 | 5.5556 | |
| ckim-gatk | INDEL | D16_PLUS | segdup | * | 91.0569 | 96.5517 | 86.1538 | 96.9253 | 56 | 2 | 56 | 9 | 2 | 22.2222 | |
| ghariani-varprowl | INDEL | I1_5 | func_cds | het | 90.3226 | 94.9153 | 86.1538 | 58.3333 | 56 | 3 | 56 | 9 | 6 | 66.6667 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 25.7312 | 15.1242 | 86.1538 | 28.5714 | 67 | 376 | 56 | 9 | 9 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 90.3980 | 95.0820 | 86.1538 | 71.6157 | 58 | 3 | 56 | 9 | 9 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.7119 | 72.4534 | 86.1538 | 53.4606 | 505 | 192 | 504 | 81 | 80 | 98.7654 | |
| ndellapenna-hhga | INDEL | D16_PLUS | map_l100_m2_e1 | * | 83.7401 | 81.4433 | 86.1702 | 87.8866 | 79 | 18 | 81 | 13 | 6 | 46.1538 | |
| qzeng-custom | INDEL | * | map_l250_m2_e0 | het | 76.6664 | 69.0476 | 86.1751 | 98.2597 | 145 | 65 | 187 | 30 | 16 | 53.3333 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m0_e0 | * | 90.5391 | 95.3650 | 86.1780 | 88.0700 | 823 | 40 | 823 | 132 | 24 | 18.1818 | |
| gduggal-bwavard | SNP | ti | map_l250_m2_e1 | * | 91.4742 | 97.4586 | 86.1821 | 92.2577 | 4947 | 129 | 4921 | 789 | 28 | 3.5488 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 84.1619 | 82.2267 | 86.1905 | 45.3886 | 7777 | 1681 | 7783 | 1247 | 1228 | 98.4763 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 91.1970 | 96.8085 | 86.2004 | 69.9943 | 455 | 15 | 456 | 73 | 58 | 79.4521 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 79.4861 | 73.7415 | 86.2013 | 48.1481 | 542 | 193 | 531 | 85 | 81 | 95.2941 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 90.2938 | 94.7900 | 86.2049 | 78.5292 | 4603 | 253 | 4568 | 731 | 64 | 8.7551 | |
| ghariani-varprowl | INDEL | I1_5 | segdup | het | 91.7878 | 98.1413 | 86.2069 | 96.5587 | 528 | 10 | 525 | 84 | 56 | 66.6667 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.5926 | 100.0000 | 86.2069 | 89.1386 | 25 | 0 | 25 | 4 | 3 | 75.0000 | |
| hfeng-pmm2 | INDEL | * | map_l250_m0_e0 | * | 90.9091 | 96.1538 | 86.2069 | 97.6404 | 75 | 3 | 75 | 12 | 2 | 16.6667 | |
| jlack-gatk | INDEL | D16_PLUS | map_l125_m1_e0 | * | 89.2857 | 92.5926 | 86.2069 | 97.0010 | 25 | 2 | 25 | 4 | 1 | 25.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 69.9301 | 58.8235 | 86.2069 | 92.6952 | 30 | 21 | 25 | 4 | 1 | 25.0000 | |
| qzeng-custom | INDEL | D6_15 | map_l150_m2_e1 | homalt | 86.2069 | 86.2069 | 86.2069 | 88.9313 | 25 | 4 | 25 | 4 | 3 | 75.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | map_l100_m0_e0 | * | 87.7193 | 89.2857 | 86.2069 | 94.9740 | 25 | 3 | 25 | 4 | 0 | 0.0000 | |
| anovak-vg | INDEL | D16_PLUS | map_l100_m1_e0 | het | 63.2911 | 50.0000 | 86.2069 | 85.6436 | 23 | 23 | 25 | 4 | 3 | 75.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | segdup | * | 64.1368 | 51.0638 | 86.2069 | 84.3243 | 24 | 23 | 25 | 4 | 4 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 71.4286 | 60.9756 | 86.2069 | 85.2041 | 25 | 16 | 25 | 4 | 4 | 100.0000 | |
| gduggal-snapfb | INDEL | * | HG002compoundhet | het | 71.1390 | 60.5520 | 86.2126 | 38.8614 | 2479 | 1615 | 23405 | 3743 | 1778 | 47.5020 | |
| gduggal-snapvard | INDEL | D1_5 | map_siren | * | 89.9255 | 93.9643 | 86.2197 | 83.0558 | 3316 | 213 | 3729 | 596 | 269 | 45.1342 | |
| gduggal-bwavard | INDEL | * | map_l150_m2_e0 | * | 90.6383 | 95.5256 | 86.2268 | 91.9474 | 1345 | 63 | 1346 | 215 | 47 | 21.8605 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1109 | 98.8558 | 86.2275 | 47.5941 | 432 | 5 | 432 | 69 | 69 | 100.0000 | |