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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
81001-81050 / 86044 show all | |||||||||||||||
| gduggal-snapfb | SNP | * | segdup | * | 98.9601 | 99.4941 | 98.4319 | 91.5712 | 27925 | 142 | 27933 | 445 | 34 | 7.6405 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 87.2890 | 97.6896 | 78.8899 | 75.7087 | 1649 | 39 | 1663 | 445 | 65 | 14.6067 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 62.8725 | 52.4099 | 78.5542 | 50.1920 | 1033 | 938 | 1630 | 445 | 427 | 95.9551 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 84.7915 | 95.5414 | 76.2159 | 71.9574 | 1200 | 56 | 1426 | 445 | 60 | 13.4831 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 87.1157 | 91.3786 | 83.2329 | 63.6787 | 2247 | 212 | 2209 | 445 | 437 | 98.2022 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.3883 | 91.3830 | 95.4836 | 39.3587 | 8643 | 815 | 9408 | 445 | 428 | 96.1798 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.1744 | 93.3669 | 91.0119 | 70.2375 | 4448 | 316 | 4506 | 445 | 188 | 42.2472 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.4849 | 99.6935 | 89.7936 | 83.3014 | 3903 | 12 | 3915 | 445 | 231 | 51.9101 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 75.7559 | 79.7506 | 72.1424 | 75.3616 | 1087 | 276 | 1155 | 446 | 264 | 59.1928 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | homalt | 85.5692 | 82.9537 | 88.3551 | 74.3676 | 3387 | 696 | 3384 | 446 | 347 | 77.8027 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 54.5815 | 78.4416 | 41.8514 | 67.3617 | 302 | 83 | 321 | 446 | 114 | 25.5605 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 61.9472 | 80.3853 | 50.3893 | 46.9303 | 459 | 112 | 453 | 446 | 414 | 92.8251 | |
| jlack-gatk | INDEL | I1_5 | * | homalt | 99.5330 | 99.8014 | 99.2660 | 55.8866 | 60308 | 120 | 60314 | 446 | 434 | 97.3094 | |
| bgallagher-sentieon | SNP | ti | map_siren | * | 99.6181 | 99.6801 | 99.5561 | 54.0168 | 100034 | 321 | 100019 | 446 | 66 | 14.7982 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | * | 99.1089 | 99.1189 | 99.0989 | 68.4487 | 49049 | 436 | 49051 | 446 | 108 | 24.2152 | |
| gduggal-bwaplat | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 89.3508 | 81.7668 | 98.4855 | 74.7866 | 28961 | 6458 | 29002 | 446 | 106 | 23.7668 | |
| gduggal-bwaplat | SNP | ti | map_siren | * | 90.8656 | 83.6301 | 99.4716 | 68.7099 | 83927 | 16428 | 83958 | 446 | 118 | 26.4574 | |
| gduggal-snapvard | INDEL | * | map_l150_m1_e0 | het | 82.1183 | 96.2573 | 71.6010 | 91.6254 | 823 | 32 | 1127 | 447 | 132 | 29.5302 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8086 | 98.8224 | 96.8153 | 66.1962 | 13595 | 162 | 13589 | 447 | 406 | 90.8277 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8086 | 98.8224 | 96.8153 | 66.1962 | 13595 | 162 | 13589 | 447 | 406 | 90.8277 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.8514 | 93.2059 | 90.5357 | 48.9295 | 878 | 64 | 4276 | 447 | 379 | 84.7875 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 77.4344 | 74.8652 | 80.1862 | 50.9245 | 1805 | 606 | 1809 | 447 | 421 | 94.1834 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 87.7018 | 87.7726 | 87.6311 | 81.7733 | 3180 | 443 | 3174 | 448 | 412 | 91.9643 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | homalt | 96.6035 | 99.0803 | 94.2476 | 38.7254 | 7326 | 68 | 7340 | 448 | 160 | 35.7143 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.5413 | 96.7290 | 88.7011 | 66.3212 | 3519 | 119 | 3517 | 448 | 445 | 99.3304 | |
| eyeh-varpipe | SNP | ti | map_l100_m1_e0 | het | 99.0514 | 99.6226 | 98.4868 | 69.7302 | 29829 | 113 | 29158 | 448 | 19 | 4.2411 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 80.9684 | 93.9086 | 71.1625 | 61.2108 | 1110 | 72 | 1108 | 449 | 440 | 97.9955 | |
| ciseli-custom | SNP | tv | map_l150_m2_e1 | homalt | 85.5896 | 82.9463 | 88.4069 | 74.3629 | 3429 | 705 | 3424 | 449 | 348 | 77.5056 | |
| jpowers-varprowl | SNP | ti | segdup | het | 97.6001 | 98.8695 | 96.3629 | 92.1336 | 11894 | 136 | 11896 | 449 | 2 | 0.4454 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9540 | 95.2267 | 96.6924 | 48.5132 | 13127 | 658 | 13126 | 449 | 442 | 98.4410 | |
| 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 | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.1835 | 98.9169 | 97.4610 | 70.8771 | 17626 | 193 | 17235 | 449 | 399 | 88.8641 | |
| astatham-gatk | INDEL | D1_5 | * | * | 99.5682 | 99.4433 | 99.6934 | 60.4898 | 145928 | 817 | 145983 | 449 | 317 | 70.6013 | |
| anovak-vg | INDEL | * | map_l150_m2_e1 | * | 72.7945 | 74.6352 | 71.0425 | 90.5099 | 1074 | 365 | 1104 | 450 | 242 | 53.7778 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 25.3240 | 74.5098 | 15.2542 | 84.3039 | 76 | 26 | 81 | 450 | 7 | 1.5556 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.6745 | 93.2968 | 96.0934 | 44.0771 | 11079 | 796 | 11069 | 450 | 425 | 94.4444 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 79.7708 | 76.3365 | 83.5286 | 61.7313 | 871 | 270 | 2282 | 450 | 243 | 54.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 22.9777 | 16.1847 | 39.5973 | 75.5015 | 319 | 1652 | 295 | 450 | 6 | 1.3333 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 22.9777 | 16.1847 | 39.5973 | 75.5015 | 319 | 1652 | 295 | 450 | 6 | 1.3333 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.6816 | 97.8606 | 97.5032 | 50.0471 | 17794 | 389 | 17573 | 450 | 107 | 23.7778 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 39.9604 | 56.2674 | 30.9816 | 39.7969 | 202 | 157 | 202 | 450 | 389 | 86.4444 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.4027 | 98.2214 | 98.5847 | 55.7301 | 31423 | 569 | 31346 | 450 | 436 | 96.8889 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.7747 | 91.3682 | 80.8266 | 73.3477 | 1990 | 188 | 1897 | 450 | 430 | 95.5556 | |
| gduggal-snapfb | INDEL | * | HG002compoundhet | hetalt | 76.0060 | 64.4003 | 92.7141 | 74.7872 | 16216 | 8964 | 5739 | 451 | 378 | 83.8137 | |
| eyeh-varpipe | SNP | tv | map_l125_m0_e0 | het | 94.8919 | 99.6364 | 90.5787 | 80.4588 | 4385 | 16 | 4336 | 451 | 9 | 1.9956 | |
| gduggal-bwavard | INDEL | * | map_l100_m1_e0 | het | 89.9219 | 98.1208 | 82.9876 | 89.4070 | 2193 | 42 | 2200 | 451 | 184 | 40.7982 | |
| cchapple-custom | INDEL | I1_5 | * | * | 99.2924 | 98.8889 | 99.6992 | 56.2734 | 148990 | 1674 | 149480 | 451 | 355 | 78.7140 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e0 | * | 90.4686 | 92.6889 | 88.3523 | 92.4226 | 3423 | 270 | 3421 | 451 | 206 | 45.6763 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 51.0719 | 55.5556 | 47.2579 | 93.7840 | 400 | 320 | 405 | 452 | 26 | 5.7522 | |