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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28201-28250 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 73.5213 | 72.9508 | 74.1007 | 51.5679 | 89 | 33 | 103 | 36 | 31 | 86.1111 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 74.4676 | 94.6746 | 61.3692 | 51.5690 | 160 | 9 | 502 | 316 | 146 | 46.2025 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | het | 97.7232 | 97.5199 | 97.9274 | 51.5698 | 20250 | 515 | 20317 | 430 | 365 | 84.8837 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4263 | 99.4533 | 99.3994 | 51.5732 | 3638 | 20 | 3641 | 22 | 17 | 77.2727 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.0941 | 94.7894 | 99.5137 | 51.5749 | 6549 | 360 | 6548 | 32 | 28 | 87.5000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3497 | 99.9156 | 98.7902 | 51.5758 | 2368 | 2 | 2368 | 29 | 29 | 100.0000 | |
| cchapple-custom | INDEL | * | tech_badpromoters | het | 98.7013 | 97.4359 | 100.0000 | 51.5789 | 38 | 1 | 46 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 80.0693 | 68.8525 | 95.6522 | 51.5789 | 42 | 19 | 88 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 55.0866 | 65.0355 | 47.7778 | 51.5804 | 917 | 493 | 1376 | 1504 | 1123 | 74.6676 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 27.4282 | 17.8862 | 58.7940 | 51.5815 | 44 | 202 | 117 | 82 | 82 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | * | homalt | 98.1988 | 99.5416 | 96.8918 | 51.5867 | 6297 | 29 | 6297 | 202 | 199 | 98.5149 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 91.6332 | 88.2406 | 95.2970 | 51.5896 | 15593 | 2078 | 16717 | 825 | 785 | 95.1515 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 91.6332 | 88.2406 | 95.2970 | 51.5896 | 15593 | 2078 | 16717 | 825 | 785 | 95.1515 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7827 | 99.6639 | 97.9169 | 51.5925 | 9489 | 32 | 9495 | 202 | 199 | 98.5149 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8771 | 100.0000 | 99.7546 | 51.5937 | 2439 | 0 | 2439 | 6 | 0 | 0.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.1538 | 98.0392 | 94.3396 | 51.5982 | 100 | 2 | 100 | 6 | 5 | 83.3333 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 43.8001 | 29.2941 | 86.7647 | 51.6014 | 249 | 601 | 236 | 36 | 27 | 75.0000 | |
| qzeng-custom | INDEL | * | * | homalt | 98.3570 | 98.7793 | 97.9383 | 51.6092 | 123644 | 1528 | 123655 | 2603 | 1560 | 59.9308 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.1971 | 91.6616 | 76.1638 | 51.6125 | 3001 | 273 | 2994 | 937 | 932 | 99.4664 | |
| gduggal-bwavard | INDEL | D1_5 | tech_badpromoters | het | 69.5652 | 100.0000 | 53.3333 | 51.6129 | 8 | 0 | 8 | 7 | 6 | 85.7143 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9556 | 99.9112 | 100.0000 | 51.6129 | 2250 | 2 | 2250 | 0 | 0 | ||
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 62.4653 | 60.2952 | 64.7975 | 51.6129 | 817 | 538 | 1040 | 565 | 411 | 72.7434 | |
| cchapple-custom | INDEL | I16_PLUS | HG002compoundhet | * | 94.6047 | 92.5805 | 96.7194 | 51.6153 | 1984 | 159 | 2506 | 85 | 81 | 95.2941 | |
| qzeng-custom | INDEL | * | HG002complexvar | homalt | 98.4127 | 98.7679 | 98.0601 | 51.6191 | 26694 | 333 | 26841 | 531 | 325 | 61.2053 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.8266 | 96.5799 | 82.2256 | 51.6201 | 15221 | 539 | 16108 | 3482 | 3306 | 94.9454 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4692 | 99.8734 | 99.0683 | 51.6226 | 1578 | 2 | 1595 | 15 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 50.1118 | 85.0427 | 35.5215 | 51.6283 | 3781 | 665 | 3804 | 6905 | 6879 | 99.6235 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8767 | 99.8821 | 99.8712 | 51.6311 | 10166 | 12 | 10084 | 13 | 11 | 84.6154 | |
| ltrigg-rtg1 | SNP | * | tech_badpromoters | * | 97.5000 | 99.3631 | 95.7055 | 51.6320 | 156 | 1 | 156 | 7 | 0 | 0.0000 | |
| bgallagher-sentieon | SNP | * | tech_badpromoters | het | 98.0132 | 96.1039 | 100.0000 | 51.6340 | 74 | 3 | 74 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | tech_badpromoters | * | 90.5660 | 84.7059 | 97.2973 | 51.6340 | 72 | 13 | 72 | 2 | 1 | 50.0000 | |
| qzeng-custom | SNP | tv | tech_badpromoters | * | 93.8212 | 95.8333 | 91.8919 | 51.6340 | 69 | 3 | 68 | 6 | 1 | 16.6667 | |
| ciseli-custom | SNP | tv | HG002compoundhet | * | 66.9226 | 84.5568 | 55.3744 | 51.6390 | 7545 | 1378 | 7573 | 6103 | 515 | 8.4385 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 92.1875 | 85.5072 | 100.0000 | 51.6393 | 59 | 10 | 59 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 84.9281 | 95.2067 | 76.6525 | 51.6405 | 2602 | 131 | 3073 | 936 | 904 | 96.5812 | |
| ciseli-custom | INDEL | I6_15 | HG002compoundhet | het | 17.3297 | 18.2692 | 16.4820 | 51.6410 | 38 | 170 | 119 | 603 | 564 | 93.5323 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 78.2874 | 71.9726 | 85.8170 | 51.6431 | 7976 | 3106 | 8120 | 1342 | 1151 | 85.7675 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8361 | 99.8770 | 99.7952 | 51.6436 | 2436 | 3 | 2437 | 5 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7153 | 99.8632 | 97.5936 | 51.6484 | 5110 | 7 | 5110 | 126 | 125 | 99.2063 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.5998 | 99.7544 | 99.4458 | 51.6487 | 10153 | 25 | 10587 | 59 | 58 | 98.3051 | |
| mlin-fermikit | INDEL | D1_5 | * | het | 97.6071 | 97.5792 | 97.6350 | 51.6497 | 85454 | 2120 | 85333 | 2067 | 1958 | 94.7267 | |
| ndellapenna-hhga | INDEL | I16_PLUS | * | hetalt | 89.6769 | 82.4118 | 98.3466 | 51.6538 | 1729 | 369 | 1725 | 29 | 24 | 82.7586 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9334 | 99.9112 | 99.9556 | 51.6538 | 2250 | 2 | 2250 | 1 | 1 | 100.0000 | |
| astatham-gatk | SNP | * | tech_badpromoters | het | 97.3333 | 94.8052 | 100.0000 | 51.6556 | 73 | 4 | 73 | 0 | 0 | ||
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 91.0850 | 84.6196 | 98.6202 | 51.6582 | 15372 | 2794 | 15367 | 215 | 153 | 71.1628 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.0850 | 84.6196 | 98.6202 | 51.6582 | 15372 | 2794 | 15367 | 215 | 153 | 71.1628 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6222 | 99.3336 | 99.9125 | 51.6616 | 25190 | 169 | 25113 | 22 | 14 | 63.6364 | |
| bgallagher-sentieon | INDEL | D6_15 | func_cds | het | 100.0000 | 100.0000 | 100.0000 | 51.6667 | 29 | 0 | 29 | 0 | 0 | ||
| dgrover-gatk | INDEL | D6_15 | func_cds | het | 100.0000 | 100.0000 | 100.0000 | 51.6667 | 29 | 0 | 29 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.9151 | 90.2558 | 95.7358 | 51.6673 | 2399 | 259 | 29209 | 1301 | 1194 | 91.7756 | |