PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28601-28650 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | * | func_cds | * | 99.3314 | 99.7753 | 98.8914 | 54.2132 | 444 | 1 | 446 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 95.9513 | 95.9677 | 95.9350 | 99.9185 | 119 | 5 | 118 | 5 | 0 | 0.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 94.2194 | 94.2529 | 94.1860 | 99.8927 | 82 | 5 | 81 | 5 | 0 | 0.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 90.5425 | 92.0000 | 89.1304 | 86.2687 | 46 | 4 | 41 | 5 | 2 | 40.0000 | |
| ckim-gatk | INDEL | * | map_l125_m0_e0 | homalt | 98.7741 | 99.2958 | 98.2578 | 88.6874 | 282 | 2 | 282 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | * | map_l150_m1_e0 | homalt | 98.8082 | 98.7013 | 98.9154 | 89.0629 | 456 | 6 | 456 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | * | map_l150_m2_e0 | homalt | 98.8554 | 98.7526 | 98.9583 | 89.9160 | 475 | 6 | 475 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.9825 | 99.0991 | 98.8662 | 76.1105 | 440 | 4 | 436 | 5 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.8135 | 96.1864 | 99.4965 | 31.6116 | 908 | 36 | 988 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3534 | 99.7835 | 98.9270 | 64.3185 | 461 | 1 | 461 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.7378 | 94.8571 | 98.6945 | 34.1924 | 332 | 18 | 378 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | * | 88.1356 | 92.8571 | 83.8710 | 97.1001 | 26 | 2 | 26 | 5 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.3378 | 87.8389 | 99.5712 | 29.6743 | 1134 | 157 | 1161 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | map_siren | homalt | 99.4864 | 99.4007 | 99.5723 | 81.4444 | 1161 | 7 | 1164 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.7147 | 100.0000 | 97.4619 | 47.3262 | 192 | 0 | 192 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m1_e0 | * | 96.1702 | 96.5812 | 95.7627 | 92.6980 | 113 | 4 | 113 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m1_e0 | het | 94.6565 | 96.8750 | 92.5373 | 94.2637 | 62 | 2 | 62 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m2_e0 | * | 96.0317 | 96.0317 | 96.0317 | 92.9688 | 121 | 5 | 121 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m2_e0 | het | 94.4444 | 95.7746 | 93.1507 | 94.4190 | 68 | 3 | 68 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m2_e1 | * | 95.6863 | 95.3125 | 96.0630 | 93.0752 | 122 | 6 | 122 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | D6_15 | map_l125_m2_e1 | het | 94.4444 | 95.7746 | 93.1507 | 94.5482 | 68 | 3 | 68 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.3832 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.1978 | 94.7154 | 97.7273 | 88.5833 | 233 | 13 | 215 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0949 | 93.7500 | 96.4789 | 89.8208 | 150 | 10 | 137 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.0545 | 97.4227 | 98.6945 | 75.5740 | 378 | 10 | 378 | 5 | 2 | 40.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5149 | 99.5000 | 97.5490 | 60.8445 | 199 | 1 | 199 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4085 | 99.1930 | 99.6249 | 78.2367 | 1352 | 11 | 1328 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5587 | 100.0000 | 99.1213 | 72.8401 | 564 | 0 | 564 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.4231 | 99.8069 | 99.0421 | 81.1416 | 517 | 1 | 517 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.4371 | 99.8117 | 99.0654 | 82.4417 | 530 | 1 | 530 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.4465 | 99.8148 | 99.0809 | 82.4799 | 539 | 1 | 539 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l250_m0_e0 | * | 86.2745 | 91.6667 | 81.4815 | 98.6855 | 22 | 2 | 22 | 5 | 1 | 20.0000 | |
| ckim-gatk | INDEL | I6_15 | HG002complexvar | het | 99.3586 | 98.9384 | 99.7824 | 59.6346 | 2330 | 25 | 2293 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.6346 | 95.5466 | 97.7477 | 80.8621 | 236 | 11 | 217 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4149 | 94.6309 | 96.2121 | 77.5128 | 141 | 8 | 127 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I6_15 | map_siren | * | 97.5207 | 96.7213 | 98.3333 | 85.9287 | 295 | 10 | 295 | 5 | 2 | 40.0000 | |
| ckim-gatk | SNP | * | * | hetalt | 98.6111 | 97.8186 | 99.4166 | 53.8999 | 852 | 19 | 852 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5563 | 99.1458 | 99.9703 | 67.1493 | 16830 | 145 | 16830 | 5 | 5 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5563 | 99.1458 | 99.9703 | 67.1493 | 16830 | 145 | 16830 | 5 | 5 | 100.0000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8976 | 100.0000 | 99.7954 | 52.3680 | 2439 | 0 | 2439 | 5 | 0 | 0.0000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8420 | 100.0000 | 99.6845 | 55.0099 | 1580 | 0 | 1580 | 5 | 0 | 0.0000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5016 | 99.4565 | 99.5467 | 86.5782 | 1098 | 6 | 1098 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4452 | 99.5833 | 99.3075 | 87.8041 | 717 | 3 | 717 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7923 | 99.6650 | 99.9200 | 46.9810 | 6247 | 21 | 6247 | 5 | 3 | 60.0000 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8184 | 99.8386 | 99.7982 | 36.6402 | 2474 | 4 | 2473 | 5 | 1 | 20.0000 | |
| ckim-gatk | SNP | ti | map_l125_m1_e0 | homalt | 77.0788 | 62.7343 | 99.9279 | 73.7914 | 6929 | 4116 | 6929 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | map_l125_m2_e0 | homalt | 77.6462 | 63.4883 | 99.9307 | 75.7176 | 7211 | 4147 | 7211 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | map_l125_m2_e1 | homalt | 77.8127 | 63.7109 | 99.9316 | 75.6597 | 7300 | 4158 | 7300 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | tv | * | hetalt | 98.6111 | 97.8186 | 99.4166 | 53.8999 | 852 | 19 | 852 | 5 | 4 | 80.0000 | |