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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66651-66700 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.9574 | 97.3744 | 96.5440 | 64.7133 | 2151 | 58 | 2151 | 77 | 74 | 96.1039 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4784 | 99.1386 | 99.8206 | 46.1563 | 6675 | 58 | 6677 | 12 | 6 | 50.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.9883 | 95.6391 | 94.3463 | 80.9074 | 1272 | 58 | 1068 | 64 | 58 | 90.6250 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7075 | 95.5178 | 100.0000 | 35.7483 | 1236 | 58 | 1348 | 0 | 0 | ||
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.3649 | 84.9741 | 98.7952 | 90.6820 | 328 | 58 | 328 | 4 | 1 | 25.0000 | |
| rpoplin-dv42 | SNP | * | segdup | het | 99.7082 | 99.6651 | 99.7514 | 90.3344 | 17259 | 58 | 17253 | 43 | 3 | 6.9767 | |
| rpoplin-dv42 | SNP | ti | HG002compoundhet | het | 99.5469 | 99.3898 | 99.7044 | 38.8720 | 9447 | 58 | 9445 | 28 | 22 | 78.5714 | |
| rpoplin-dv42 | SNP | ti | map_l250_m1_e0 | het | 98.2113 | 98.0458 | 98.3773 | 88.2203 | 2910 | 58 | 2910 | 48 | 29 | 60.4167 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | homalt | 99.7077 | 99.5096 | 99.9066 | 69.9014 | 11769 | 58 | 11769 | 11 | 8 | 72.7273 | |
| raldana-dualsentieon | SNP | * | segdup | * | 99.5928 | 99.7934 | 99.3931 | 89.8391 | 28009 | 58 | 28003 | 171 | 10 | 5.8480 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 31.6999 | 78.9855 | 19.8291 | 89.3462 | 218 | 58 | 232 | 938 | 21 | 2.2388 | |
| gduggal-snapplat | INDEL | D16_PLUS | segdup | * | 0.0000 | 0.0000 | 0.0000 | 0 | 58 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D6_15 | map_l150_m2_e1 | * | 45.0221 | 31.7647 | 77.2727 | 96.4912 | 27 | 58 | 17 | 5 | 1 | 20.0000 | |
| gduggal-snapplat | INDEL | D6_15 | segdup | het | 48.4621 | 36.9565 | 70.3704 | 96.6376 | 34 | 58 | 19 | 8 | 1 | 12.5000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 43.9535 | 83.9779 | 29.7665 | 62.1084 | 304 | 58 | 306 | 722 | 718 | 99.4460 | |
| gduggal-snapfb | INDEL | D16_PLUS | segdup | * | 0.0000 | 0.0000 | 0.0000 | 0 | 58 | 0 | 0 | 0 | |||
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 1.6949 | 0.0000 | 0.0000 | 1 | 58 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 3.3333 | 0.0000 | 0.0000 | 2 | 58 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 88.8822 | 83.2370 | 95.3488 | 70.9740 | 288 | 58 | 287 | 14 | 13 | 92.8571 | |
| ghariani-varprowl | INDEL | I6_15 | segdup | * | 72.0984 | 66.8571 | 78.2313 | 93.2039 | 117 | 58 | 115 | 32 | 32 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.1522 | 95.1464 | 99.2443 | 33.7229 | 1137 | 58 | 1182 | 9 | 8 | 88.8889 | |
| anovak-vg | INDEL | D1_5 | map_l150_m1_e0 | het | 80.6909 | 87.9668 | 74.5267 | 89.8052 | 424 | 58 | 433 | 148 | 55 | 37.1622 | |
| bgallagher-sentieon | SNP | * | map_l150_m1_e0 | homalt | 99.6712 | 99.4855 | 99.8575 | 68.3134 | 11215 | 58 | 11215 | 16 | 12 | 75.0000 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5825 | 99.2217 | 99.9459 | 39.6327 | 7394 | 58 | 7391 | 4 | 1 | 25.0000 | |
| astatham-gatk | SNP | tv | map_l125_m1_e0 | homalt | 99.4259 | 99.0102 | 99.8451 | 64.3015 | 5802 | 58 | 5802 | 9 | 6 | 66.6667 | |
| astatham-gatk | SNP | tv | map_l125_m2_e0 | homalt | 99.4410 | 99.0361 | 99.8492 | 66.8223 | 5959 | 58 | 5959 | 9 | 6 | 66.6667 | |
| astatham-gatk | SNP | tv | map_l125_m2_e1 | homalt | 99.4462 | 99.0451 | 99.8506 | 66.8391 | 6016 | 58 | 6016 | 9 | 6 | 66.6667 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.0448 | 95.6587 | 96.4340 | 58.7351 | 1278 | 58 | 1271 | 47 | 25 | 53.1915 | |
| astatham-gatk | INDEL | * | map_l100_m0_e0 | * | 96.7251 | 96.2892 | 97.1649 | 87.6728 | 1505 | 58 | 1508 | 44 | 9 | 20.4545 | |
| astatham-gatk | INDEL | * | map_l150_m2_e0 | * | 96.6049 | 95.8807 | 97.3400 | 91.1929 | 1350 | 58 | 1354 | 37 | 7 | 18.9189 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 37.5202 | 27.1605 | 60.6557 | 60.8974 | 22 | 59 | 37 | 24 | 17 | 70.8333 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e0 | * | 53.4759 | 49.1379 | 58.6538 | 81.9130 | 57 | 59 | 61 | 43 | 25 | 58.1395 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e1 | * | 53.2425 | 49.1379 | 58.0952 | 82.0819 | 57 | 59 | 61 | 44 | 25 | 56.8182 | |
| anovak-vg | INDEL | I6_15 | segdup | het | 38.0775 | 28.9157 | 55.7377 | 91.0688 | 24 | 59 | 34 | 27 | 13 | 48.1481 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.2004 | 96.2658 | 96.1350 | 51.4737 | 1521 | 59 | 1567 | 63 | 25 | 39.6825 | |
| bgallagher-sentieon | SNP | tv | map_l125_m1_e0 | het | 98.8364 | 99.4173 | 98.2622 | 74.9493 | 10067 | 59 | 10065 | 178 | 22 | 12.3596 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e0 | het | 98.8667 | 99.4350 | 98.3049 | 76.2296 | 10383 | 59 | 10381 | 179 | 22 | 12.2905 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | het | 98.8786 | 99.4409 | 98.3226 | 76.2835 | 10494 | 59 | 10492 | 179 | 22 | 12.2905 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1381 | 98.8474 | 99.4304 | 72.0835 | 5060 | 59 | 5237 | 30 | 24 | 80.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 59 | 0 | 0 | 0 | |||
| astatham-gatk | SNP | * | map_l250_m1_e0 | homalt | 98.6256 | 97.6045 | 99.6683 | 85.3151 | 2404 | 59 | 2404 | 8 | 7 | 87.5000 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7920 | 99.4303 | 96.2068 | 45.3054 | 10298 | 59 | 10906 | 430 | 320 | 74.4186 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.3254 | 96.9477 | 97.7059 | 65.2032 | 1874 | 59 | 1874 | 44 | 43 | 97.7273 | |
| asubramanian-gatk | INDEL | D1_5 | HG002compoundhet | het | 95.2389 | 96.5856 | 93.9292 | 78.7201 | 1669 | 59 | 1671 | 108 | 103 | 95.3704 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.3602 | 96.1713 | 98.5789 | 73.8003 | 1482 | 59 | 1873 | 27 | 17 | 62.9630 | |
| asubramanian-gatk | SNP | ti | func_cds | * | 99.6805 | 99.5721 | 99.7892 | 27.6472 | 13728 | 59 | 13726 | 29 | 1 | 3.4483 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.6619 | 66.8539 | 87.1429 | 65.7702 | 119 | 59 | 122 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.1505 | 98.5769 | 91.9543 | 85.8273 | 4087 | 59 | 4103 | 359 | 47 | 13.0919 | |
| gduggal-bwafb | SNP | tv | map_l100_m2_e0 | homalt | 99.6083 | 99.3597 | 99.8582 | 65.9435 | 9155 | 59 | 9155 | 13 | 7 | 53.8462 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.2638 | 96.1738 | 96.3539 | 73.1963 | 1483 | 59 | 1797 | 68 | 52 | 76.4706 | |