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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12401-12450 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6082 | 99.8778 | 99.3401 | 60.0690 | 55563 | 68 | 55552 | 369 | 30 | 8.1301 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4306 | 99.8701 | 98.9950 | 61.8984 | 35373 | 46 | 35362 | 359 | 20 | 5.5710 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.0000 | 92.3077 | 100.0000 | 82.3529 | 12 | 1 | 12 | 0 | 0 | ||
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9232 | 99.8960 | 99.9505 | 56.3257 | 20178 | 21 | 20178 | 10 | 10 | 100.0000 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.7884 | 98.3155 | 99.2658 | 69.8244 | 92858 | 1591 | 106946 | 791 | 672 | 84.9558 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8427 | 98.3427 | 99.3479 | 69.0114 | 47471 | 800 | 76325 | 501 | 389 | 77.6447 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 95.5114 | 0.0000 | 0.0000 | 14725 | 692 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3690 | 99.6782 | 99.0618 | 71.6714 | 30662 | 99 | 30621 | 290 | 283 | 97.5862 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9428 | 98.4681 | 99.4221 | 74.5651 | 63444 | 987 | 63485 | 369 | 305 | 82.6558 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1330 | 98.7273 | 99.5420 | 75.3696 | 32813 | 423 | 32819 | 151 | 102 | 67.5497 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9370 | 94.9441 | 99.0153 | 65.4795 | 8826 | 470 | 8849 | 88 | 83 | 94.3182 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4891 | 99.5708 | 99.4077 | 75.9619 | 21805 | 94 | 21817 | 130 | 120 | 92.3077 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 86.5741 | 0 | 0 | 0 | 58 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 88.5350 | 0 | 0 | 0 | 36 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 71.4286 | 0 | 0 | 0 | 2 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 81.9820 | 0 | 0 | 0 | 20 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 0.0000 | 66.6667 | 0.0000 | 75.5627 | 2 | 1 | 0 | 304 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 66.6667 | 0.0000 | 75.7212 | 2 | 1 | 0 | 202 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 66.6667 | 0 | 0 | 0 | 4 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 75.5000 | 0 | 0 | 0 | 98 | 0 | 0.0000 | ||
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5168 | 99.0808 | 99.9567 | 54.7993 | 27702 | 257 | 27701 | 12 | 5 | 41.6667 | |
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3009 | 98.6611 | 99.9489 | 57.4118 | 17612 | 239 | 17611 | 9 | 2 | 22.2222 | |
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 87.8049 | 5 | 1 | 5 | 0 | 0 | ||
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9009 | 99.8317 | 99.9703 | 49.2989 | 10085 | 17 | 10085 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2746 | 98.1228 | 98.4270 | 77.7694 | 92676 | 1773 | 96110 | 1536 | 892 | 58.0729 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4217 | 98.4028 | 98.4406 | 75.5838 | 47500 | 771 | 49303 | 781 | 332 | 42.5096 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.7294 | 94.6488 | 98.9035 | 60.3171 | 14592 | 825 | 15424 | 171 | 158 | 92.3977 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.7949 | 99.4246 | 98.1731 | 74.1057 | 30584 | 177 | 31383 | 584 | 402 | 68.8356 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5183 | 97.1076 | 97.9326 | 72.3189 | 3458 | 103 | 3458 | 73 | 57 | 78.0822 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.8698 | 97.4170 | 96.3288 | 83.1947 | 1320 | 35 | 1207 | 46 | 34 | 73.9130 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1850 | 95.5951 | 98.8287 | 37.6825 | 1237 | 57 | 1350 | 16 | 14 | 87.5000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.7939 | 98.7939 | 98.7939 | 70.6564 | 901 | 11 | 901 | 11 | 9 | 81.8182 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4245 | 98.9414 | 99.9124 | 64.7733 | 27385 | 293 | 27376 | 24 | 14 | 58.3333 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2005 | 98.5314 | 99.8788 | 66.3539 | 17310 | 258 | 17301 | 21 | 11 | 52.3810 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.0000 | 92.3077 | 100.0000 | 82.3529 | 12 | 1 | 12 | 0 | 0 | ||
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8165 | 99.6633 | 99.9702 | 61.6256 | 10063 | 34 | 10063 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 0.0000 | 100.0000 | 0.0000 | 78.5021 | 1 | 0 | 0 | 155 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 100.0000 | 0.0000 | 78.2857 | 1 | 0 | 0 | 114 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 80.0000 | 0 | 0 | 0 | 2 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 79.0323 | 0 | 0 | 0 | 39 | 0 | 0.0000 | ||
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 15.2225 | 9.4654 | 38.8554 | 56.6013 | 108 | 1033 | 129 | 203 | 109 | 53.6946 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 13.0521 | 7.5688 | 47.3684 | 59.8945 | 33 | 403 | 72 | 80 | 25 | 31.2500 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 4.6312 | 0.0000 | 0.0000 | 27 | 556 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 35.0904 | 39.3443 | 31.6667 | 53.3679 | 48 | 74 | 57 | 123 | 84 | 68.2927 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 57.0334 | 48.7504 | 68.7072 | 56.9745 | 1736 | 1825 | 1706 | 777 | 550 | 70.7851 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 62.4653 | 60.2952 | 64.7975 | 51.6129 | 817 | 538 | 1040 | 565 | 411 | 72.7434 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 20.0155 | 0.0000 | 0.0000 | 259 | 1035 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 74.0703 | 72.3684 | 75.8542 | 64.2217 | 660 | 252 | 666 | 212 | 139 | 65.5660 | |
| anovak-vg | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 72.8701 | 70.9790 | 74.8646 | 68.2103 | 67039 | 27410 | 79629 | 26735 | 20426 | 76.4017 | |
| anovak-vg | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 75.7760 | 77.8397 | 73.8189 | 67.4300 | 37574 | 10697 | 51936 | 18420 | 13343 | 72.4376 | |