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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
80801-80850 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 76.0681 | 70.4167 | 82.7057 | 61.6372 | 338 | 142 | 1186 | 248 | 176 | 70.9677 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5538 | 96.9440 | 94.2029 | 48.6379 | 1142 | 36 | 3055 | 188 | 176 | 93.6170 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.7116 | 95.4096 | 98.0496 | 64.9238 | 15339 | 738 | 15333 | 305 | 176 | 57.7049 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.7116 | 95.4096 | 98.0496 | 64.9238 | 15339 | 738 | 15333 | 305 | 176 | 57.7049 | |
| eyeh-varpipe | INDEL | * | map_l100_m1_e0 | * | 94.5716 | 93.6419 | 95.5200 | 92.2711 | 3358 | 228 | 4776 | 224 | 176 | 78.5714 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9622 | 97.8431 | 98.0816 | 45.4687 | 9254 | 204 | 9254 | 181 | 176 | 97.2376 | |
| jlack-gatk | SNP | * | map_l150_m2_e0 | het | 93.6840 | 98.8973 | 88.9927 | 86.5727 | 19911 | 222 | 19905 | 2462 | 176 | 7.1487 | |
| jlack-gatk | SNP | ti | map_l100_m2_e0 | het | 96.4036 | 99.2424 | 93.7226 | 78.7202 | 30390 | 232 | 30383 | 2035 | 176 | 8.6487 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.3416 | 88.0522 | 94.8864 | 61.9636 | 3508 | 476 | 3507 | 189 | 176 | 93.1217 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | * | 96.2606 | 94.1648 | 98.4519 | 64.4321 | 11635 | 721 | 11638 | 183 | 176 | 96.1749 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.7392 | 98.1151 | 99.3713 | 57.1912 | 30816 | 592 | 30820 | 195 | 176 | 90.2564 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.7392 | 98.1151 | 99.3713 | 57.1912 | 30816 | 592 | 30820 | 195 | 176 | 90.2564 | |
| gduggal-snapvard | INDEL | D6_15 | * | homalt | 45.1606 | 30.1454 | 89.9777 | 38.5773 | 1907 | 4419 | 1616 | 180 | 176 | 97.7778 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 5.1744 | 2.8363 | 29.4574 | 72.6502 | 101 | 3460 | 114 | 273 | 176 | 64.4689 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 9.1482 | 5.4613 | 28.1579 | 72.1408 | 74 | 1281 | 107 | 273 | 176 | 64.4689 | |
| cchapple-custom | SNP | * | map_l125_m0_e0 | * | 96.1705 | 96.0794 | 96.2618 | 77.2988 | 18625 | 760 | 18618 | 723 | 176 | 24.3430 | |
| eyeh-varpipe | SNP | * | HG002compoundhet | * | 97.2195 | 99.1054 | 95.4041 | 44.2893 | 25591 | 231 | 16939 | 816 | 176 | 21.5686 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 68.3650 | 71.1864 | 65.7588 | 23.2836 | 42 | 17 | 338 | 176 | 176 | 100.0000 | |
| jlack-gatk | SNP | ti | map_l100_m2_e1 | het | 96.4266 | 99.2506 | 93.7588 | 78.7315 | 30728 | 232 | 30721 | 2045 | 177 | 8.6553 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0806 | 99.8938 | 98.2806 | 45.8961 | 10346 | 11 | 10346 | 181 | 177 | 97.7901 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 59.0700 | 91.8519 | 43.5331 | 43.8938 | 124 | 11 | 138 | 179 | 177 | 98.8827 | |
| anovak-vg | INDEL | I1_5 | map_l100_m0_e0 | * | 58.1032 | 59.3002 | 56.9536 | 86.9940 | 322 | 221 | 344 | 260 | 177 | 68.0769 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.3679 | 93.1480 | 77.1005 | 68.0245 | 3317 | 244 | 3377 | 1003 | 177 | 17.6471 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 79.8661 | 82.5564 | 77.3455 | 75.6274 | 549 | 116 | 676 | 198 | 177 | 89.3939 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.1163 | 94.9599 | 95.2731 | 65.4635 | 3674 | 195 | 3628 | 180 | 177 | 98.3333 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 47.1967 | 32.7646 | 84.3521 | 58.6869 | 1037 | 2128 | 1035 | 192 | 177 | 92.1875 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 47.1992 | 32.7962 | 84.1592 | 58.8707 | 1038 | 2127 | 1036 | 195 | 177 | 90.7692 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 60.4335 | 56.1688 | 65.3989 | 55.6013 | 692 | 540 | 705 | 373 | 177 | 47.4531 | |
| gduggal-snapvard | INDEL | I1_5 | * | homalt | 92.2555 | 85.9022 | 99.6235 | 34.4127 | 51909 | 8519 | 51074 | 193 | 178 | 92.2280 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 52.7157 | 43.0290 | 68.0310 | 66.2410 | 1574 | 2084 | 2194 | 1031 | 178 | 17.2648 | |
| qzeng-custom | SNP | tv | map_l125_m0_e0 | het | 81.8738 | 72.6880 | 93.7170 | 91.2462 | 3199 | 1202 | 3192 | 214 | 178 | 83.1776 | |
| ndellapenna-hhga | INDEL | I1_5 | * | het | 99.3796 | 99.2245 | 99.5353 | 57.8169 | 78428 | 613 | 78394 | 366 | 178 | 48.6339 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.0091 | 80.8442 | 83.2080 | 53.2969 | 996 | 236 | 996 | 201 | 178 | 88.5572 | |
| ckim-isaac | INDEL | I16_PLUS | HG002compoundhet | * | 61.2497 | 48.1568 | 84.1205 | 44.7593 | 1032 | 1111 | 1033 | 195 | 178 | 91.2821 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.6109 | 85.8533 | 95.9267 | 79.8715 | 13236 | 2181 | 4239 | 180 | 178 | 98.8889 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.1916 | 95.2534 | 93.1533 | 76.2686 | 5940 | 296 | 5864 | 431 | 178 | 41.2993 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 80.7110 | 78.7684 | 82.7519 | 62.8376 | 857 | 231 | 854 | 178 | 178 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.8144 | 64.9791 | 93.9211 | 77.3415 | 9498 | 5119 | 9502 | 615 | 178 | 28.9431 | |
| gduggal-bwaplat | INDEL | D1_5 | * | homalt | 94.9240 | 90.7227 | 99.5332 | 62.2451 | 44387 | 4539 | 44353 | 208 | 178 | 85.5769 | |
| jlack-gatk | SNP | * | map_l150_m2_e1 | het | 93.7014 | 98.9098 | 89.0141 | 86.6201 | 20141 | 222 | 20135 | 2485 | 178 | 7.1630 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1969 | 98.0419 | 98.3525 | 52.6692 | 10865 | 217 | 10865 | 182 | 178 | 97.8022 | |
| jmaeng-gatk | SNP | ti | * | * | 99.6502 | 99.4959 | 99.8049 | 21.8521 | 2074998 | 10513 | 2074939 | 4056 | 178 | 4.3886 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.2310 | 89.4309 | 83.2523 | 73.2130 | 1210 | 143 | 1198 | 241 | 178 | 73.8589 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.2521 | 92.5164 | 80.7824 | 44.1095 | 2114 | 171 | 2127 | 506 | 178 | 35.1779 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9495 | 96.9056 | 99.0161 | 33.0779 | 17694 | 565 | 18416 | 183 | 178 | 97.2678 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.5788 | 95.2991 | 95.8600 | 66.1112 | 4237 | 209 | 4191 | 181 | 178 | 98.3425 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0434 | 93.0771 | 95.0299 | 54.7829 | 3657 | 272 | 3652 | 191 | 179 | 93.7173 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7823 | 92.5681 | 95.0288 | 54.7425 | 3637 | 292 | 3632 | 190 | 179 | 94.2105 | |