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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66851-66900 / 86044 show all | |||||||||||||||
| ckim-gatk | SNP | ti | map_l150_m2_e0 | homalt | 73.0167 | 57.5236 | 99.9316 | 81.2297 | 4381 | 3235 | 4381 | 3 | 2 | 66.6667 | |
| ckim-gatk | SNP | ti | map_l150_m2_e1 | homalt | 73.1394 | 57.6758 | 99.9324 | 81.1976 | 4437 | 3256 | 4437 | 3 | 2 | 66.6667 | |
| ckim-gatk | SNP | tv | map_siren | hetalt | 87.2483 | 80.2469 | 95.5882 | 82.7848 | 65 | 16 | 65 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 85.2572 | 77.2727 | 95.0820 | 73.0088 | 102 | 30 | 116 | 6 | 4 | 66.6667 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 56.0000 | 43.7500 | 77.7778 | 99.2094 | 7 | 9 | 21 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l125_m0_e0 | homalt | 97.8873 | 97.8873 | 97.8873 | 88.7703 | 278 | 6 | 278 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l250_m1_e0 | homalt | 96.2963 | 95.4128 | 97.1963 | 95.1496 | 104 | 5 | 104 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e0 | homalt | 96.4912 | 95.6522 | 97.3451 | 95.5424 | 110 | 5 | 110 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e1 | homalt | 96.5217 | 95.6897 | 97.3684 | 95.6322 | 111 | 5 | 111 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.0391 | 99.4096 | 96.7059 | 82.8744 | 1347 | 8 | 1233 | 42 | 28 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3521 | 100.0000 | 98.7124 | 71.6889 | 230 | 0 | 230 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 95.3020 | 94.6667 | 95.9459 | 64.9289 | 71 | 4 | 71 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2332 | 96.8504 | 97.6190 | 79.0698 | 123 | 4 | 123 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6017 | 99.5025 | 99.7012 | 65.7688 | 1000 | 5 | 1001 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6526 | 99.6524 | 99.6528 | 63.6057 | 860 | 3 | 861 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.3396 | 100.0000 | 89.2857 | 92.7273 | 25 | 0 | 25 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6602 | 96.7890 | 98.5472 | 85.8707 | 422 | 14 | 407 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.2609 | 99.1228 | 97.4138 | 85.9564 | 113 | 1 | 113 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m1_e0 | homalt | 99.3902 | 99.6942 | 99.0881 | 83.5088 | 326 | 1 | 326 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | homalt | 99.4152 | 99.7067 | 99.1254 | 84.7216 | 340 | 1 | 340 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e1 | homalt | 99.4186 | 99.7085 | 99.1304 | 84.9608 | 342 | 1 | 342 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 97.7192 | 97.1591 | 98.2857 | 92.7023 | 171 | 5 | 172 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m1_e0 | homalt | 98.9950 | 99.4949 | 98.5000 | 87.0801 | 197 | 1 | 197 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.0099 | 99.5025 | 98.5222 | 88.5634 | 200 | 1 | 200 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.0244 | 99.5098 | 98.5437 | 88.6501 | 203 | 1 | 203 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l250_m1_e0 | * | 95.6938 | 94.3396 | 97.0874 | 96.3358 | 100 | 6 | 100 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l250_m2_e0 | * | 95.9641 | 94.6903 | 97.2727 | 96.6616 | 107 | 6 | 107 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_l250_m2_e1 | * | 96.0000 | 94.7368 | 97.2973 | 96.7401 | 108 | 6 | 108 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | map_siren | homalt | 99.6298 | 99.7525 | 99.5074 | 78.6951 | 1209 | 3 | 1212 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I6_15 | map_siren | * | 97.1901 | 96.3934 | 98.0000 | 85.1852 | 294 | 11 | 294 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.7836 | 97.1503 | 98.4252 | 91.2111 | 375 | 11 | 375 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.6407 | 97.4638 | 97.8182 | 91.2809 | 269 | 7 | 269 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.9143 | 99.8827 | 99.9458 | 56.3849 | 11071 | 13 | 11067 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | map_l125_m0_e0 | homalt | 99.3639 | 98.9124 | 99.8196 | 67.9886 | 6639 | 73 | 6639 | 12 | 8 | 66.6667 | |
| dgrover-gatk | SNP | ti | map_l250_m1_e0 | homalt | 99.0596 | 98.3199 | 99.8105 | 85.5645 | 1580 | 27 | 1580 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e0 | homalt | 99.1074 | 98.3991 | 99.8260 | 86.5878 | 1721 | 28 | 1721 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e1 | homalt | 99.1191 | 98.4199 | 99.8283 | 86.6233 | 1744 | 28 | 1744 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m0_e0 | homalt | 99.2811 | 98.7952 | 99.7719 | 75.6572 | 1312 | 16 | 1312 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m1_e0 | homalt | 99.4146 | 98.9863 | 99.8466 | 69.3080 | 3906 | 40 | 3906 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | homalt | 99.4343 | 99.0203 | 99.8518 | 71.6158 | 4043 | 40 | 4043 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e1 | homalt | 99.4413 | 99.0324 | 99.8537 | 71.5870 | 4094 | 40 | 4094 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l250_m0_e0 | homalt | 98.1818 | 97.9275 | 98.4375 | 92.5983 | 189 | 4 | 189 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.2515 | 91.2014 | 89.3212 | 56.4841 | 1078 | 104 | 1079 | 129 | 86 | 66.6667 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 74.7966 | 60.2857 | 98.5075 | 44.9315 | 211 | 139 | 198 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.4183 | 93.3511 | 95.5102 | 59.6597 | 702 | 50 | 702 | 33 | 22 | 66.6667 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 97.3333 | 98.6486 | 96.0526 | 81.1414 | 73 | 1 | 73 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | homalt | 80.0000 | 100.0000 | 66.6667 | 99.6005 | 6 | 0 | 6 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 77.2448 | 63.4300 | 98.7526 | 34.5578 | 503 | 290 | 475 | 6 | 4 | 66.6667 | |