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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26201-26250 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D1_5 | map_l125_m2_e0 | het | 97.6378 | 97.3822 | 97.8947 | 85.3565 | 744 | 20 | 744 | 16 | 4 | 25.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l125_m2_e1 | het | 97.6562 | 97.4026 | 97.9112 | 85.4539 | 750 | 20 | 750 | 16 | 4 | 25.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l150_m2_e1 | * | 97.8696 | 97.4293 | 98.3139 | 88.2398 | 758 | 20 | 758 | 13 | 6 | 46.1538 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 89.1712 | 90.4306 | 87.9464 | 73.4911 | 189 | 20 | 197 | 27 | 10 | 37.0370 | |
| qzeng-custom | INDEL | D6_15 | map_l125_m2_e0 | * | 84.0880 | 84.1270 | 84.0491 | 91.3252 | 106 | 20 | 137 | 26 | 6 | 23.0769 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | het | 64.8870 | 57.4468 | 74.5413 | 60.7207 | 27 | 20 | 325 | 111 | 71 | 63.9640 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 55.9649 | 69.6970 | 46.7532 | 65.8537 | 46 | 20 | 72 | 82 | 24 | 29.2683 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 73.1635 | 81.4815 | 66.3866 | 60.7261 | 88 | 20 | 158 | 80 | 21 | 26.2500 | |
| qzeng-custom | INDEL | I1_5 | map_l250_m1_e0 | het | 77.2881 | 66.6667 | 91.9355 | 98.3812 | 40 | 20 | 57 | 5 | 4 | 80.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.4384 | 95.9432 | 96.9388 | 58.1197 | 473 | 20 | 475 | 15 | 12 | 80.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.4707 | 95.9016 | 89.2767 | 52.5444 | 468 | 20 | 3555 | 427 | 343 | 80.3279 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9190 | 99.2554 | 96.6182 | 68.9966 | 2666 | 20 | 2657 | 93 | 4 | 4.3011 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.6095 | 92.7536 | 79.4872 | 92.6630 | 256 | 20 | 279 | 72 | 9 | 12.5000 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3593 | 99.4891 | 99.2298 | 79.0524 | 3895 | 20 | 3865 | 30 | 20 | 66.6667 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.5900 | 99.3241 | 97.8667 | 64.6435 | 2939 | 20 | 2936 | 64 | 4 | 6.2500 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | map_l100_m2_e1 | * | 87.4735 | 79.3814 | 97.4026 | 83.5118 | 77 | 20 | 75 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l150_m2_e1 | het | 97.6691 | 96.1686 | 99.2172 | 80.3989 | 502 | 20 | 507 | 4 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.6802 | 96.8254 | 96.5354 | 62.6690 | 610 | 20 | 613 | 22 | 7 | 31.8182 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m0_e0 | * | 97.5715 | 96.3168 | 98.8593 | 76.8994 | 523 | 20 | 520 | 6 | 1 | 16.6667 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l150_m2_e0 | * | 97.6462 | 96.1464 | 99.1935 | 86.0635 | 499 | 20 | 492 | 4 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l150_m2_e1 | * | 97.7011 | 96.2335 | 99.2141 | 86.1081 | 511 | 20 | 505 | 4 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.5345 | 91.9028 | 97.3214 | 70.5650 | 227 | 20 | 218 | 6 | 2 | 33.3333 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 84.0961 | 80.3922 | 88.1579 | 92.2449 | 82 | 20 | 67 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7012 | 99.7281 | 99.6744 | 30.0294 | 7335 | 20 | 7346 | 24 | 4 | 16.6667 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5635 | 99.5014 | 99.6257 | 47.9205 | 3991 | 20 | 3992 | 15 | 4 | 26.6667 | |
| ndellapenna-hhga | SNP | ti | map_l150_m0_e0 | homalt | 99.5641 | 99.2756 | 99.8543 | 71.8779 | 2741 | 20 | 2741 | 4 | 4 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l150_m1_e0 | homalt | 99.6826 | 99.4932 | 99.8728 | 70.1019 | 3926 | 20 | 3926 | 5 | 4 | 80.0000 | |
| ndellapenna-hhga | SNP | tv | map_l150_m2_e0 | homalt | 99.6933 | 99.5102 | 99.8771 | 72.6980 | 4063 | 20 | 4063 | 5 | 4 | 80.0000 | |
| ndellapenna-hhga | SNP | tv | map_l150_m2_e1 | homalt | 99.6971 | 99.5162 | 99.8786 | 72.6929 | 4114 | 20 | 4114 | 5 | 4 | 80.0000 | |
| mlin-fermikit | INDEL | D6_15 | segdup | hetalt | 74.3590 | 59.1837 | 100.0000 | 89.2193 | 29 | 20 | 29 | 0 | 0 | ||
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | het | 6.2171 | 57.4468 | 3.2864 | 65.0533 | 27 | 20 | 14 | 412 | 412 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | HG002compoundhet | homalt | 49.1644 | 93.9210 | 33.2972 | 76.0021 | 309 | 20 | 307 | 615 | 607 | 98.6992 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.0318 | 94.2197 | 95.8580 | 61.6780 | 326 | 20 | 324 | 14 | 10 | 71.4286 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 43.8101 | 60.7843 | 34.2466 | 81.0390 | 31 | 20 | 25 | 48 | 46 | 95.8333 | |
| mlin-fermikit | INDEL | I6_15 | map_l125_m1_e0 | * | 71.1252 | 62.2642 | 82.9268 | 83.4677 | 33 | 20 | 34 | 7 | 6 | 85.7143 | |
| mlin-fermikit | INDEL | I6_15 | map_l125_m2_e0 | * | 71.1252 | 62.2642 | 82.9268 | 86.1017 | 33 | 20 | 34 | 7 | 6 | 85.7143 | |
| mlin-fermikit | INDEL | I6_15 | map_l125_m2_e1 | * | 71.1252 | 62.2642 | 82.9268 | 86.6013 | 33 | 20 | 34 | 7 | 6 | 85.7143 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 74.0343 | 69.6970 | 78.9474 | 95.0607 | 46 | 20 | 45 | 12 | 3 | 25.0000 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6953 | 99.4211 | 99.9709 | 62.6075 | 3435 | 20 | 3435 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.8022 | 98.1618 | 97.4453 | 67.6027 | 1068 | 20 | 1068 | 28 | 24 | 85.7143 | |
| anovak-vg | INDEL | D1_5 | map_l250_m1_e0 | het | 72.2766 | 81.9820 | 64.6259 | 95.9781 | 91 | 20 | 95 | 52 | 22 | 42.3077 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 57.2317 | 53.4884 | 61.5385 | 74.3421 | 23 | 20 | 24 | 15 | 8 | 53.3333 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 8.6957 | 4.7619 | 50.0000 | 75.0000 | 1 | 20 | 1 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 29.4118 | 42.8571 | 22.3881 | 56.2092 | 15 | 20 | 15 | 52 | 24 | 46.1538 | |
| bgallagher-sentieon | INDEL | I16_PLUS | HG002complexvar | hetalt | 96.7847 | 94.0299 | 99.7059 | 69.0909 | 315 | 20 | 339 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.3553 | 99.2639 | 99.4469 | 87.8858 | 2697 | 20 | 2697 | 15 | 13 | 86.6667 | |
| bgallagher-sentieon | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1348 | 99.8900 | 98.3909 | 39.6771 | 18163 | 20 | 18160 | 297 | 4 | 1.3468 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7876 | 99.6312 | 99.9445 | 71.5069 | 5403 | 20 | 5403 | 3 | 3 | 100.0000 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7876 | 99.6312 | 99.9445 | 71.5069 | 5403 | 20 | 5403 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3198 | 99.0645 | 99.5765 | 41.0214 | 2118 | 20 | 2116 | 9 | 2 | 22.2222 | |