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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72951-73000 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D1_5 | map_l100_m1_e0 | het | 89.6970 | 83.6228 | 96.7227 | 89.7617 | 1011 | 198 | 1151 | 39 | 27 | 69.2308 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m2_e0 | het | 89.9373 | 83.9968 | 96.7820 | 89.9588 | 1055 | 201 | 1203 | 40 | 27 | 67.5000 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m2_e1 | het | 89.9622 | 84.0694 | 96.7434 | 89.9976 | 1066 | 202 | 1218 | 41 | 27 | 65.8537 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m1_e0 | * | 86.3838 | 78.0331 | 96.7359 | 91.0029 | 849 | 239 | 978 | 33 | 27 | 81.8182 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e0 | * | 86.6114 | 78.3027 | 96.8927 | 91.2636 | 895 | 248 | 1029 | 33 | 27 | 81.8182 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e1 | * | 86.7845 | 78.5653 | 96.9245 | 91.3188 | 909 | 248 | 1040 | 33 | 27 | 81.8182 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 95.2238 | 96.6140 | 93.8731 | 40.3394 | 428 | 15 | 429 | 28 | 27 | 96.4286 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 89.8965 | 92.6829 | 87.2727 | 88.8945 | 190 | 15 | 192 | 28 | 27 | 96.4286 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 89.8965 | 92.6829 | 87.2727 | 88.8945 | 190 | 15 | 192 | 28 | 27 | 96.4286 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 81.9762 | 69.7710 | 99.3570 | 62.1268 | 4143 | 1795 | 4172 | 27 | 27 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 44.0143 | 35.8696 | 56.9444 | 58.6207 | 33 | 59 | 41 | 31 | 27 | 87.0968 | |
| qzeng-custom | SNP | tv | segdup | * | 98.3829 | 98.6521 | 98.1152 | 93.4371 | 8417 | 115 | 8381 | 161 | 27 | 16.7702 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7452 | 99.9341 | 99.5570 | 56.8831 | 6068 | 4 | 6068 | 27 | 27 | 100.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 79.8224 | 95.4545 | 68.5897 | 91.7504 | 105 | 5 | 107 | 49 | 27 | 55.1020 | |
| ghariani-varprowl | SNP | * | map_l250_m0_e0 | het | 91.3804 | 97.1448 | 86.2618 | 95.0573 | 1463 | 43 | 1463 | 233 | 27 | 11.5880 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m1_e0 | het | 85.1353 | 81.5550 | 89.0443 | 91.4683 | 986 | 223 | 1146 | 141 | 27 | 19.1489 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 43.8001 | 29.2941 | 86.7647 | 51.6014 | 249 | 601 | 236 | 36 | 27 | 75.0000 | |
| gduggal-snapplat | SNP | ti | map_l250_m0_e0 | het | 84.2801 | 77.7302 | 92.0354 | 96.9671 | 726 | 208 | 728 | 63 | 27 | 42.8571 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 67.0378 | 96.3964 | 51.3872 | 89.5473 | 428 | 16 | 426 | 403 | 27 | 6.6998 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 72.4427 | 98.5075 | 57.2852 | 93.2156 | 462 | 7 | 460 | 343 | 27 | 7.8717 | |
| gduggal-snapplat | INDEL | * | segdup | * | 77.9673 | 71.4789 | 85.7514 | 96.5099 | 1827 | 729 | 1980 | 329 | 27 | 8.2067 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 71.8529 | 57.2932 | 96.3338 | 35.0041 | 762 | 568 | 762 | 29 | 27 | 93.1034 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m0_e0 | * | 89.9579 | 95.1613 | 85.2941 | 90.0943 | 295 | 15 | 493 | 85 | 27 | 31.7647 | |
| gduggal-snapvard | INDEL | I6_15 | HG002complexvar | homalt | 45.0525 | 29.6785 | 93.4732 | 26.9165 | 360 | 853 | 401 | 28 | 27 | 96.4286 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | * | 60.8583 | 72.0000 | 52.7027 | 87.7888 | 18 | 7 | 39 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | het | 63.8563 | 93.3333 | 48.5294 | 87.8571 | 14 | 1 | 33 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 37.8203 | 79.7927 | 24.7836 | 90.1732 | 308 | 78 | 315 | 956 | 27 | 2.8243 | |
| gduggal-snapvard | SNP | * | map_l125_m1_e0 | homalt | 97.9102 | 96.1077 | 99.7817 | 66.1808 | 16247 | 658 | 15999 | 35 | 27 | 77.1429 | |
| ghariani-varprowl | INDEL | * | map_l125_m0_e0 | het | 90.1652 | 97.6150 | 83.7719 | 93.3586 | 573 | 14 | 573 | 111 | 27 | 24.3243 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m1_e0 | * | 91.7326 | 95.8640 | 87.9427 | 88.9869 | 1043 | 45 | 1043 | 143 | 27 | 18.8811 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m2_e0 | * | 91.9463 | 95.8880 | 88.3159 | 89.5819 | 1096 | 47 | 1096 | 145 | 27 | 18.6207 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m2_e1 | het | 91.0832 | 98.8312 | 84.4617 | 91.0642 | 761 | 9 | 761 | 140 | 27 | 19.2857 | |
| gduggal-snapfb | INDEL | D1_5 | map_siren | * | 96.5488 | 96.9963 | 96.1054 | 82.0770 | 3423 | 106 | 3430 | 139 | 27 | 19.4245 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 40.9756 | 28.1879 | 75.0000 | 50.6849 | 42 | 107 | 81 | 27 | 27 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | map_l100_m1_e0 | homalt | 89.7866 | 85.3041 | 94.7664 | 81.8274 | 505 | 87 | 507 | 28 | 27 | 96.4286 | |
| anovak-vg | INDEL | D6_15 | map_l100_m1_e0 | * | 69.8276 | 62.7907 | 78.6408 | 85.3172 | 162 | 96 | 162 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e0 | * | 69.8453 | 62.5000 | 79.1469 | 85.8199 | 165 | 99 | 167 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e1 | * | 69.0673 | 61.0909 | 79.4393 | 85.8746 | 168 | 107 | 170 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 21.1214 | 16.8539 | 28.2828 | 55.6054 | 30 | 148 | 28 | 71 | 27 | 38.0282 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.6772 | 96.0184 | 99.3942 | 25.6555 | 4582 | 190 | 4594 | 28 | 27 | 96.4286 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.6923 | 100.0000 | 91.7404 | 70.3412 | 311 | 0 | 311 | 28 | 27 | 96.4286 | |
| astatham-gatk | SNP | * | map_l125_m1_e0 | het | 85.6838 | 75.1515 | 99.6496 | 79.7424 | 21337 | 7055 | 21331 | 75 | 27 | 36.0000 | |
| astatham-gatk | SNP | * | map_l125_m2_e0 | het | 85.8236 | 75.3598 | 99.6616 | 80.7499 | 22094 | 7224 | 22088 | 75 | 27 | 36.0000 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | het | 85.8279 | 75.3644 | 99.6653 | 80.7852 | 22338 | 7302 | 22332 | 75 | 27 | 36.0000 | |
| astatham-gatk | SNP | * | map_l150_m2_e0 | het | 86.3036 | 76.1635 | 99.5583 | 83.9104 | 15334 | 4799 | 15328 | 68 | 27 | 39.7059 | |
| astatham-gatk | SNP | * | map_l150_m2_e1 | het | 86.2859 | 76.1332 | 99.5631 | 83.9622 | 15503 | 4860 | 15497 | 68 | 27 | 39.7059 | |
| astatham-gatk | SNP | ti | map_l150_m2_e0 | * | 91.3750 | 84.3165 | 99.7232 | 79.9461 | 17295 | 3217 | 17291 | 48 | 27 | 56.2500 | |
| astatham-gatk | SNP | ti | map_l150_m2_e1 | * | 91.3679 | 84.3025 | 99.7259 | 80.0126 | 17470 | 3253 | 17466 | 48 | 27 | 56.2500 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.5262 | 96.9639 | 94.1304 | 83.3091 | 511 | 16 | 433 | 27 | 27 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3955 | 88.2236 | 96.9815 | 64.0909 | 884 | 118 | 996 | 31 | 27 | 87.0968 | |