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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31651-31700 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.8499 | 98.2717 | 97.4317 | 68.9817 | 3696 | 65 | 4173 | 110 | 107 | 97.2727 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5281 | 99.6497 | 97.4315 | 67.4470 | 569 | 2 | 569 | 15 | 15 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.3948 | 97.3583 | 97.4313 | 62.8424 | 3796 | 103 | 3793 | 100 | 40 | 40.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7461 | 88.4908 | 97.4313 | 66.6799 | 1630 | 212 | 1631 | 43 | 33 | 76.7442 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.5269 | 91.7910 | 97.4308 | 60.3759 | 492 | 44 | 493 | 13 | 11 | 84.6154 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002compoundhet | * | 95.0754 | 92.8327 | 97.4292 | 36.3885 | 8147 | 629 | 8148 | 215 | 212 | 98.6047 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1314 | 98.8438 | 97.4291 | 67.5197 | 14448 | 169 | 14060 | 371 | 345 | 92.9919 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3796 | 95.3528 | 97.4288 | 66.7644 | 3878 | 189 | 3865 | 102 | 94 | 92.1569 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 95.6348 | 93.9058 | 97.4286 | 67.0123 | 339 | 22 | 341 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002complexvar | homalt | 98.6168 | 99.8353 | 97.4277 | 55.0578 | 1212 | 2 | 1212 | 32 | 32 | 100.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6321 | 97.8377 | 97.4273 | 73.5072 | 3484 | 77 | 3484 | 92 | 64 | 69.5652 | |
| qzeng-custom | INDEL | D1_5 | map_siren | het | 92.9621 | 88.8889 | 97.4265 | 85.9785 | 2024 | 253 | 2120 | 56 | 32 | 57.1429 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m2_e0 | * | 97.0663 | 96.7102 | 97.4251 | 83.8811 | 1852 | 63 | 2308 | 61 | 36 | 59.0164 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | het | 92.3834 | 87.8381 | 97.4248 | 82.5144 | 40756 | 5643 | 40745 | 1077 | 78 | 7.2423 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.7152 | 96.0167 | 97.4238 | 54.7331 | 8027 | 333 | 8055 | 213 | 202 | 94.8357 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.7152 | 96.0167 | 97.4238 | 54.7331 | 8027 | 333 | 8055 | 213 | 202 | 94.8357 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.7435 | 96.0727 | 97.4237 | 57.9207 | 16977 | 694 | 16979 | 449 | 417 | 92.8731 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.7435 | 96.0727 | 97.4237 | 57.9207 | 16977 | 694 | 16979 | 449 | 417 | 92.8731 | |
| bgallagher-sentieon | INDEL | * | map_l150_m1_e0 | * | 97.9979 | 98.5800 | 97.4227 | 90.0883 | 1319 | 19 | 1323 | 35 | 7 | 20.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.9275 | 98.4375 | 97.4227 | 86.2069 | 378 | 6 | 378 | 10 | 2 | 20.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l125_m0_e0 | het | 97.6690 | 97.9167 | 97.4227 | 90.2951 | 188 | 4 | 189 | 5 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 70.6542 | 55.4252 | 97.4227 | 64.6630 | 189 | 152 | 189 | 5 | 5 | 100.0000 | |
| jpowers-varprowl | SNP | tv | map_siren | het | 97.6371 | 97.8538 | 97.4214 | 66.9739 | 27995 | 614 | 27995 | 741 | 114 | 15.3846 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 65.8938 | 49.7835 | 97.4194 | 62.0098 | 230 | 232 | 302 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.3317 | 95.2681 | 97.4194 | 82.1360 | 906 | 45 | 906 | 24 | 19 | 79.1667 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1461 | 96.8750 | 97.4186 | 69.7659 | 1736 | 56 | 1736 | 46 | 39 | 84.7826 | |
| ckim-gatk | SNP | ti | map_l100_m0_e0 | het | 86.7938 | 78.2593 | 97.4176 | 85.5089 | 10943 | 3040 | 10940 | 290 | 35 | 12.0690 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | * | 97.3999 | 97.3828 | 97.4170 | 66.7553 | 1600 | 43 | 1584 | 42 | 31 | 73.8095 | |
| ghariani-varprowl | INDEL | * | map_l125_m0_e0 | homalt | 95.1351 | 92.9577 | 97.4170 | 87.2290 | 264 | 20 | 264 | 7 | 3 | 42.8571 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.0940 | 96.7742 | 97.4160 | 59.9171 | 510 | 17 | 1508 | 40 | 36 | 90.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2661 | 91.3134 | 97.4160 | 66.6942 | 9198 | 875 | 9048 | 240 | 203 | 84.5833 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.3930 | 99.3902 | 97.4155 | 59.5008 | 489 | 3 | 490 | 13 | 11 | 84.6154 | |
| qzeng-custom | SNP | tv | map_l125_m1_e0 | * | 84.7104 | 74.9376 | 97.4144 | 82.6672 | 12002 | 4014 | 11981 | 318 | 271 | 85.2201 | |
| rpoplin-dv42 | INDEL | * | map_l250_m2_e1 | homalt | 97.4138 | 97.4138 | 97.4138 | 95.3036 | 113 | 3 | 113 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | * | map_l250_m2_e0 | homalt | 97.8355 | 98.2609 | 97.4138 | 94.1971 | 113 | 2 | 113 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.2609 | 99.1228 | 97.4138 | 85.6258 | 113 | 1 | 113 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.6549 | 93.9583 | 97.4138 | 82.6607 | 451 | 29 | 452 | 12 | 11 | 91.6667 | |
| 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 | |
| egarrison-hhga | INDEL | * | map_l250_m2_e1 | homalt | 97.4138 | 97.4138 | 97.4138 | 95.4277 | 113 | 3 | 113 | 3 | 1 | 33.3333 | |
| jmaeng-gatk | INDEL | D6_15 | map_l125_m1_e0 | * | 96.9957 | 96.5812 | 97.4138 | 92.7318 | 113 | 4 | 113 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | INDEL | D6_15 | map_l125_m1_e0 | * | 94.7920 | 92.3077 | 97.4138 | 88.3300 | 108 | 9 | 113 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | INDEL | * | map_l250_m2_e0 | homalt | 97.8355 | 98.2609 | 97.4138 | 95.2692 | 113 | 2 | 113 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l250_m2_e0 | homalt | 97.8355 | 98.2609 | 97.4138 | 95.3432 | 113 | 2 | 113 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | * | map_l250_m2_e1 | homalt | 97.4138 | 97.4138 | 97.4138 | 94.6445 | 113 | 3 | 113 | 3 | 2 | 66.6667 | |
| bgallagher-sentieon | INDEL | * | map_l125_m1_e0 | het | 97.9174 | 98.4270 | 97.4132 | 88.3493 | 1314 | 21 | 1318 | 35 | 5 | 14.2857 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.7218 | 88.4618 | 97.4128 | 51.1450 | 15763 | 2056 | 30197 | 802 | 660 | 82.2943 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.0092 | 98.6133 | 97.4125 | 67.2319 | 640 | 9 | 640 | 17 | 17 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | map_l250_m1_e0 | het | 98.1612 | 98.9218 | 97.4121 | 90.4001 | 2936 | 32 | 2936 | 78 | 16 | 20.5128 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | * | 94.7676 | 92.2629 | 97.4120 | 66.1892 | 11400 | 956 | 11405 | 303 | 301 | 99.3399 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5527 | 99.7211 | 97.4114 | 61.5908 | 715 | 2 | 715 | 19 | 18 | 94.7368 | |