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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54801-54850 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I1_5 | map_l250_m0_e0 | homalt | 94.7368 | 100.0000 | 90.0000 | 96.8750 | 9 | 0 | 9 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | segdup | het | 91.7231 | 98.6989 | 85.6683 | 96.3967 | 531 | 7 | 532 | 89 | 1 | 1.1236 | |
| jlack-gatk | INDEL | I6_15 | HG002complexvar | hetalt | 95.3861 | 91.2510 | 99.9136 | 55.5641 | 1116 | 107 | 1157 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | func_cds | * | 97.6744 | 97.6744 | 97.6744 | 42.6667 | 42 | 1 | 42 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | func_cds | homalt | 96.7742 | 100.0000 | 93.7500 | 40.7407 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 90.9909 | 83.7736 | 99.5690 | 47.3923 | 444 | 86 | 462 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.2857 | 97.1751 | 99.4220 | 74.4838 | 172 | 5 | 172 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 90.5668 | 83.1956 | 99.3711 | 46.1017 | 302 | 61 | 316 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 76.9231 | 65.2174 | 93.7500 | 58.4416 | 60 | 32 | 60 | 4 | 1 | 25.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.9417 | 63.8554 | 96.7742 | 29.5455 | 53 | 30 | 60 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.8217 | 92.4731 | 99.4220 | 70.1209 | 172 | 14 | 172 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 0.0000 | 0.0000 | 96.4286 | 0 | 0 | 0 | 1 | 1 | 100.0000 | ||
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4012 | 99.2823 | 99.5204 | 47.6788 | 415 | 3 | 415 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5789 | 99.5781 | 99.5798 | 24.6835 | 236 | 1 | 237 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | map_siren | het | 91.9861 | 92.3077 | 91.6667 | 87.8583 | 132 | 11 | 132 | 12 | 1 | 8.3333 | |
| jlack-gatk | INDEL | I6_15 | segdup | * | 95.7507 | 96.5714 | 94.9438 | 93.8621 | 169 | 6 | 169 | 9 | 1 | 11.1111 | |
| jlack-gatk | INDEL | I6_15 | segdup | homalt | 97.8723 | 97.8723 | 97.8723 | 92.5750 | 46 | 1 | 46 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | HG002compoundhet | hetalt | 99.6512 | 99.4200 | 99.8834 | 22.4231 | 857 | 5 | 857 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | func_cds | * | 99.3020 | 99.9614 | 98.6513 | 31.6355 | 18143 | 7 | 18140 | 248 | 1 | 0.4032 | |
| jlack-gatk | SNP | * | func_cds | het | 98.8875 | 99.9731 | 97.8251 | 36.6500 | 11158 | 3 | 11155 | 248 | 1 | 0.4032 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 92.3077 | 92.3077 | 92.3077 | 81.4286 | 12 | 1 | 12 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2666 | 99.8474 | 98.6925 | 59.1977 | 3925 | 6 | 3925 | 52 | 1 | 1.9231 | |
| 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 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.4485 | 99.9742 | 98.9283 | 61.3587 | 3877 | 1 | 3877 | 42 | 1 | 2.3810 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1650 | 100.0000 | 98.3438 | 63.2517 | 2494 | 0 | 2494 | 42 | 1 | 2.3810 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.9091 | 100.0000 | 83.3333 | 62.5000 | 5 | 0 | 5 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | map_l250_m0_e0 | hetalt | 0.0000 | 0.0000 | 98.3051 | 0 | 0 | 0 | 1 | 1 | 100.0000 | ||
| jlack-gatk | SNP | * | map_l250_m1_e0 | hetalt | 75.0000 | 75.0000 | 75.0000 | 96.4912 | 3 | 1 | 3 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | hetalt | 80.0000 | 80.0000 | 80.0000 | 96.3504 | 4 | 1 | 4 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | map_l250_m2_e1 | hetalt | 80.0000 | 80.0000 | 80.0000 | 96.3504 | 4 | 1 | 4 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | segdup | hetalt | 93.3333 | 100.0000 | 87.5000 | 98.2533 | 7 | 0 | 7 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | func_cds | * | 99.4443 | 99.9565 | 98.9373 | 29.0994 | 13781 | 6 | 13779 | 148 | 1 | 0.6757 | |
| jlack-gatk | SNP | ti | func_cds | het | 99.1254 | 99.9765 | 98.2886 | 33.6861 | 8502 | 2 | 8500 | 148 | 1 | 0.6757 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 83.3333 | 83.3333 | 83.3333 | 86.0465 | 5 | 1 | 5 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6270 | 99.8753 | 99.3798 | 50.2161 | 4006 | 5 | 4006 | 25 | 1 | 4.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9318 | 99.9318 | 99.9318 | 43.0237 | 1465 | 1 | 1465 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8636 | 97.9730 | 99.7706 | 84.0117 | 435 | 9 | 435 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4764 | 99.2167 | 99.7375 | 82.5868 | 380 | 3 | 380 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7031 | 99.4668 | 99.9405 | 63.6364 | 1679 | 9 | 1679 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 66.6667 | 100.0000 | 50.0000 | 75.0000 | 1 | 0 | 1 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9373 | 99.9248 | 99.9498 | 33.7544 | 3984 | 3 | 3984 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4965 | 99.7175 | 99.2765 | 38.0786 | 2471 | 7 | 2470 | 18 | 1 | 5.5556 | |
| jlack-gatk | SNP | ti | map_l250_m0_e0 | hetalt | 0.0000 | 0.0000 | 97.2222 | 0 | 0 | 0 | 1 | 1 | 100.0000 | ||
| jlack-gatk | SNP | ti | map_l250_m0_e0 | homalt | 97.5439 | 95.6422 | 99.5227 | 91.4751 | 417 | 19 | 417 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | ti | map_l250_m1_e0 | hetalt | 75.0000 | 75.0000 | 75.0000 | 94.4444 | 3 | 1 | 3 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | map_l250_m2_e0 | hetalt | 80.0000 | 80.0000 | 80.0000 | 94.0476 | 4 | 1 | 4 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | map_l250_m2_e1 | hetalt | 80.0000 | 80.0000 | 80.0000 | 94.0476 | 4 | 1 | 4 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | segdup | hetalt | 80.0000 | 100.0000 | 66.6667 | 98.9324 | 2 | 0 | 2 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | tv | HG002compoundhet | hetalt | 99.6512 | 99.4200 | 99.8834 | 22.4231 | 857 | 5 | 857 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 92.3077 | 92.3077 | 92.3077 | 81.4286 | 12 | 1 | 12 | 1 | 1 | 100.0000 | |