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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77251-77300 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.2339 | 99.3295 | 95.2250 | 57.6340 | 11407 | 77 | 11407 | 572 | 562 | 98.2517 | |
| gduggal-bwafb | INDEL | D16_PLUS | * | * | 85.9986 | 80.3656 | 92.4807 | 53.1498 | 5452 | 1332 | 5633 | 458 | 450 | 98.2533 | |
| eyeh-varpipe | INDEL | D1_5 | * | homalt | 95.4519 | 99.1150 | 92.0499 | 59.2107 | 48493 | 433 | 48444 | 4184 | 4111 | 98.2553 | |
| ghariani-varprowl | INDEL | D6_15 | * | * | 61.5999 | 58.5275 | 65.0128 | 56.9372 | 15271 | 10821 | 15265 | 8215 | 8072 | 98.2593 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.3491 | 46.0834 | 48.6863 | 59.5527 | 14743 | 17249 | 14732 | 15527 | 15257 | 98.2611 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.6929 | 96.8651 | 88.8653 | 43.0098 | 4604 | 149 | 4597 | 576 | 566 | 98.2639 | |
| cchapple-custom | INDEL | I6_15 | HG002compoundhet | * | 95.3148 | 93.5278 | 97.1715 | 34.8185 | 8208 | 568 | 9894 | 288 | 283 | 98.2639 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 67.7028 | 91.6754 | 53.6688 | 45.2639 | 10528 | 956 | 14570 | 12578 | 12360 | 98.2668 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 80.5008 | 99.2225 | 67.7227 | 54.9332 | 8295 | 65 | 8615 | 4106 | 4035 | 98.2708 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 80.5008 | 99.2225 | 67.7227 | 54.9332 | 8295 | 65 | 8615 | 4106 | 4035 | 98.2708 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3940 | 99.7649 | 97.0603 | 61.7981 | 11457 | 27 | 11457 | 347 | 341 | 98.2709 | |
| eyeh-varpipe | INDEL | I1_5 | * | homalt | 96.1261 | 97.6964 | 94.6055 | 51.8219 | 59036 | 1392 | 58978 | 3363 | 3305 | 98.2753 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 29.7872 | 24.6479 | 37.6344 | 33.0935 | 35 | 107 | 35 | 58 | 57 | 98.2759 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 85.5129 | 76.5088 | 96.9190 | 34.7374 | 3651 | 1121 | 3649 | 116 | 114 | 98.2759 | |
| jli-custom | INDEL | * | HG002compoundhet | hetalt | 96.5598 | 93.5624 | 99.7556 | 52.2097 | 23559 | 1621 | 23678 | 58 | 57 | 98.2759 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1651 | 96.1994 | 98.1505 | 57.1994 | 3088 | 122 | 3078 | 58 | 57 | 98.2759 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4536 | 93.4690 | 99.6351 | 39.9267 | 15614 | 1091 | 15838 | 58 | 57 | 98.2759 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4536 | 93.4690 | 99.6351 | 39.9267 | 15614 | 1091 | 15838 | 58 | 57 | 98.2759 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7701 | 99.9578 | 97.6102 | 56.2071 | 2369 | 1 | 2369 | 58 | 57 | 98.2759 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7701 | 99.9578 | 97.6102 | 56.2071 | 2369 | 1 | 2369 | 58 | 57 | 98.2759 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.0148 | 97.6827 | 88.7726 | 47.1861 | 10117 | 240 | 10097 | 1277 | 1255 | 98.2772 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 74.4023 | 70.1058 | 79.2599 | 38.2733 | 14439 | 6157 | 14671 | 3839 | 3773 | 98.2808 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 77.4574 | 91.9436 | 66.9147 | 52.7787 | 3458 | 303 | 6476 | 3202 | 3147 | 98.2823 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 77.4574 | 91.9436 | 66.9147 | 52.7787 | 3458 | 303 | 6476 | 3202 | 3147 | 98.2823 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 56.4553 | 51.6684 | 62.2197 | 60.5704 | 16228 | 15180 | 16207 | 9841 | 9672 | 98.2827 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 56.4553 | 51.6684 | 62.2197 | 60.5704 | 16228 | 15180 | 16207 | 9841 | 9672 | 98.2827 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 38.7872 | 35.8879 | 42.1961 | 62.4776 | 1152 | 2058 | 1149 | 1574 | 1547 | 98.2846 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.5111 | 88.7732 | 77.0743 | 58.5831 | 1961 | 248 | 1960 | 583 | 573 | 98.2847 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 45.3446 | 44.0478 | 46.7201 | 60.8982 | 16695 | 21207 | 16673 | 19014 | 18688 | 98.2855 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 79.4291 | 78.9108 | 79.9542 | 56.7822 | 681 | 182 | 698 | 175 | 172 | 98.2857 | |
| dgrover-gatk | INDEL | * | HG002compoundhet | het | 93.5069 | 98.4612 | 89.0273 | 79.7555 | 4031 | 63 | 3789 | 467 | 459 | 98.2869 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 85.1147 | 96.8338 | 75.9259 | 61.8824 | 367 | 12 | 369 | 117 | 115 | 98.2906 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002compoundhet | * | 95.3045 | 93.6144 | 97.0566 | 64.5995 | 11567 | 789 | 11574 | 351 | 345 | 98.2906 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.3899 | 99.9450 | 96.8825 | 62.1062 | 3636 | 2 | 3636 | 117 | 115 | 98.2906 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 51.3936 | 42.2407 | 65.6103 | 66.2441 | 558 | 763 | 559 | 293 | 288 | 98.2935 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 73.0113 | 70.9589 | 75.1858 | 71.6028 | 67020 | 27429 | 66956 | 22098 | 21721 | 98.2940 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.3706 | 96.6600 | 84.8496 | 55.8282 | 9203 | 318 | 9196 | 1642 | 1614 | 98.2948 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.0536 | 99.7374 | 96.4257 | 55.6216 | 9496 | 25 | 9496 | 352 | 346 | 98.2955 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.3208 | 43.7811 | 51.4831 | 46.1266 | 7994 | 10265 | 7984 | 7524 | 7396 | 98.2988 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 75.7026 | 69.8630 | 82.6075 | 47.3461 | 1377 | 594 | 3073 | 647 | 636 | 98.2998 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 75.7026 | 69.8630 | 82.6075 | 47.3461 | 1377 | 594 | 3073 | 647 | 636 | 98.2998 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.5998 | 99.7544 | 99.4458 | 51.6487 | 10153 | 25 | 10587 | 59 | 58 | 98.3051 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 87.3841 | 93.4028 | 82.0941 | 65.3887 | 538 | 38 | 541 | 118 | 116 | 98.3051 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 45.1608 | 33.2536 | 70.3518 | 57.5693 | 139 | 279 | 140 | 59 | 58 | 98.3051 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002compoundhet | homalt | 90.7042 | 97.8723 | 84.5144 | 83.9037 | 322 | 7 | 322 | 59 | 58 | 98.3051 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1334 | 94.7850 | 99.6011 | 59.6178 | 14613 | 804 | 14733 | 59 | 58 | 98.3051 | |
| hfeng-pmm2 | INDEL | I1_5 | * | homalt | 99.7668 | 99.8262 | 99.7075 | 52.8322 | 60323 | 105 | 60327 | 177 | 174 | 98.3051 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 87.7339 | 100.0000 | 78.1481 | 67.6259 | 211 | 0 | 211 | 59 | 58 | 98.3051 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |