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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
45651-45700 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 66.0309 | 61.2472 | 71.6250 | 49.8874 | 10823 | 6848 | 10834 | 4292 | 4156 | 96.8313 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 66.0268 | 75.3467 | 58.7588 | 41.5789 | 489 | 160 | 1174 | 824 | 725 | 87.9854 | |
| jmaeng-gatk | SNP | ti | map_l150_m0_e0 | homalt | 66.0199 | 49.2937 | 99.9266 | 83.9216 | 1361 | 1400 | 1361 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l150_m1_e0 | * | 65.9997 | 49.5333 | 98.8657 | 90.7313 | 9764 | 9948 | 9762 | 112 | 2 | 1.7857 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 65.9821 | 77.5633 | 57.4100 | 52.3175 | 13821 | 3998 | 35430 | 26284 | 22200 | 84.4620 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 65.9794 | 77.7328 | 57.3134 | 76.8487 | 192 | 55 | 192 | 143 | 141 | 98.6014 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 65.9704 | 49.6410 | 98.3092 | 51.1216 | 484 | 491 | 407 | 7 | 4 | 57.1429 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e0 | * | 65.9681 | 49.6257 | 98.3589 | 92.1554 | 5635 | 5720 | 5634 | 94 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 65.9654 | 55.6526 | 80.9698 | 74.3202 | 8669 | 6908 | 8633 | 2029 | 1680 | 82.7994 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 65.9412 | 85.6091 | 53.6220 | 35.4284 | 4069 | 684 | 4049 | 3502 | 3279 | 93.6322 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 65.9384 | 80.0000 | 56.0811 | 49.8305 | 108 | 27 | 83 | 65 | 61 | 93.8462 | |
| gduggal-snapfb | INDEL | C1_5 | HG002complexvar | het | 65.9341 | 85.7143 | 53.5714 | 70.5263 | 6 | 1 | 15 | 13 | 3 | 23.0769 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 65.9107 | 59.0529 | 74.5704 | 50.3413 | 212 | 147 | 217 | 74 | 67 | 90.5405 | |
| ciseli-custom | SNP | * | HG002compoundhet | het | 65.9081 | 78.7276 | 56.6789 | 49.8597 | 11162 | 3016 | 11240 | 8591 | 230 | 2.6772 | |
| 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 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 65.8913 | 84.0000 | 54.2056 | 64.5695 | 42 | 8 | 58 | 49 | 46 | 93.8776 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 65.8825 | 97.2660 | 49.8107 | 91.6259 | 925 | 26 | 921 | 928 | 61 | 6.5733 | |
| asubramanian-gatk | SNP | ti | map_siren | hetalt | 65.8824 | 49.1228 | 100.0000 | 83.6257 | 28 | 29 | 28 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I6_15 | HG002compoundhet | het | 65.8766 | 65.8654 | 65.8879 | 86.4385 | 137 | 71 | 141 | 73 | 16 | 21.9178 | |
| qzeng-custom | INDEL | I1_5 | map_l250_m0_e0 | * | 65.8625 | 54.1667 | 84.0000 | 99.1992 | 13 | 11 | 21 | 4 | 3 | 75.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 65.8537 | 49.2027 | 99.5392 | 51.5625 | 216 | 223 | 216 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 65.8532 | 55.5178 | 80.9170 | 72.3914 | 654 | 524 | 653 | 154 | 116 | 75.3247 | |
| gduggal-bwafb | INDEL | I16_PLUS | HG002complexvar | * | 65.8380 | 50.7257 | 93.7759 | 46.3252 | 664 | 645 | 678 | 45 | 44 | 97.7778 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m2_e0 | * | 65.8291 | 50.0000 | 96.3235 | 84.3858 | 132 | 132 | 131 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | homalt | 65.8246 | 49.0764 | 99.9263 | 84.8914 | 1355 | 1406 | 1355 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002compoundhet | hetalt | 65.8129 | 49.3191 | 98.8822 | 29.8693 | 4020 | 4131 | 3450 | 39 | 30 | 76.9231 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m1_e0 | * | 65.8098 | 50.0000 | 96.2406 | 83.4577 | 129 | 129 | 128 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | * | map_l250_m1_e0 | * | 65.7952 | 49.5082 | 98.0519 | 96.9691 | 151 | 154 | 151 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l125_m0_e0 | homalt | 65.7804 | 49.0314 | 99.9093 | 59.9855 | 2202 | 2289 | 2202 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | I16_PLUS | map_siren | * | 65.7764 | 70.9302 | 61.3208 | 81.7556 | 61 | 25 | 65 | 41 | 5 | 12.1951 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 65.7662 | 77.6219 | 57.0522 | 44.3331 | 11346 | 3271 | 31729 | 23885 | 20828 | 87.2012 | |
| ciseli-custom | SNP | tv | map_l250_m1_e0 | * | 65.7644 | 60.3702 | 72.2172 | 91.9134 | 1598 | 1049 | 1596 | 614 | 128 | 20.8469 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | homalt | 65.7563 | 49.0021 | 99.9197 | 70.0457 | 3732 | 3884 | 3732 | 3 | 3 | 100.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 65.7529 | 52.8540 | 86.9801 | 38.4187 | 963 | 859 | 481 | 72 | 43 | 59.7222 | |
| anovak-vg | INDEL | * | map_l250_m2_e0 | het | 65.7491 | 68.0952 | 63.5593 | 96.7649 | 143 | 67 | 150 | 86 | 29 | 33.7209 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 65.7441 | 83.6158 | 54.1667 | 62.4609 | 148 | 29 | 195 | 165 | 113 | 68.4848 | |
| ndellapenna-hhga | INDEL | D6_15 | * | hetalt | 65.7378 | 49.3394 | 98.4629 | 43.6387 | 4033 | 4141 | 3459 | 54 | 41 | 75.9259 | |
| anovak-vg | INDEL | D16_PLUS | HG002complexvar | het | 65.7371 | 54.8329 | 82.0546 | 48.1457 | 607 | 500 | 631 | 138 | 95 | 68.8406 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m0_e0 | het | 65.7317 | 61.6667 | 70.3704 | 79.5455 | 37 | 23 | 38 | 16 | 9 | 56.2500 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 65.7303 | 76.4706 | 57.6355 | 72.3810 | 117 | 36 | 117 | 86 | 73 | 84.8837 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 65.7233 | 50.4831 | 94.1441 | 78.8168 | 209 | 205 | 209 | 13 | 8 | 61.5385 | |
| ckim-isaac | SNP | ti | map_l150_m2_e1 | homalt | 65.7188 | 48.9666 | 99.8939 | 70.0833 | 3767 | 3926 | 3767 | 4 | 4 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.7143 | 54.7619 | 82.1429 | 95.6923 | 23 | 19 | 23 | 5 | 0 | 0.0000 | |
| ciseli-custom | INDEL | * | map_l125_m0_e0 | * | 65.7143 | 59.9773 | 72.6648 | 92.6716 | 529 | 353 | 529 | 199 | 111 | 55.7789 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m0_e0 | * | 65.7143 | 69.6970 | 62.1622 | 90.1857 | 23 | 10 | 23 | 14 | 7 | 50.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 65.7127 | 54.1731 | 83.4992 | 45.7734 | 1058 | 895 | 1007 | 199 | 131 | 65.8291 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m1_e0 | het | 65.6975 | 86.6667 | 52.8986 | 82.1244 | 26 | 4 | 73 | 65 | 50 | 76.9231 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 65.6904 | 70.9091 | 61.1872 | 88.2131 | 117 | 48 | 134 | 85 | 29 | 34.1176 | |