Mercurial > repos > nml > gnali
view test-data/gnomadv3_results/Nonessential_Host_Genes_Detailed.txt @ 7:2b1154ae7e21 draft default tip
"planemo upload for repository https://github.com/phac-nml/gnali/ commit c3a811e4bb8ba8a718047c3324809175ad23291b"
| author | nml |
|---|---|
| date | Thu, 29 Jul 2021 19:17:40 +0000 |
| parents | |
| children |
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Chromosome Position_Start RSID Reference_Allele Alternate_Allele Score Quality LoF_Variant LoF_Annotation HGNC_Symbol Ensembl Code HGVSc african-AC african-AN african-AF ashkenazi-jewish-AC ashkenazi-jewish-AN ashkenazi-jewish-AF european-non-finnish-AC european-non-finnish-AN european-non-finnish-AF finnish-AC finnish-AN finnish-AF south-asian-AC south-asian-AN south-asian-AF latino-AC latino-AN latino-AF east-asian-AC east-asian-AN east-asian-AF other-AC other-AN other-AF XY-AC XY-AN XY-AF XX-AC XX-AN XX-AF chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000265379.10:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 256076 NM_001278298.1:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 256076 NM_153264.6:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 256076 XM_011512621.2:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 256076 XM_011512622.2:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130395447 rs115380050 C T . PASS T stop_gained COL6A5 256076 XM_011512623.2:c.3550C>T 753 41434 1.8173500000e-02 0 3470 0.0000000000e+00 3 68032 4.4096900000e-05 0 10606 0.0000000000e+00 2 4832 4.1390700000e-04 26 15270 1.7026900000e-03 0 5200 0.0000000000e+00 5 2090 2.3923400000e-03 354 74330 4.7625500000e-03 435 77830 5.5891000000e-03 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 ENSG00000172752 ENST00000265379.10:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 256076 NM_001278298.1:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 256076 NM_153264.6:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 256076 XM_011512621.2:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 256076 XM_011512622.2:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130405586 rs373650908 A G . PASS G splice_acceptor_variant COL6A5 256076 XM_011512623.2:c.4282-2A>G 0 41374 0.0000000000e+00 0 3470 0.0000000000e+00 0 68012 0.0000000000e+00 0 10596 0.0000000000e+00 0 4814 0.0000000000e+00 0 15260 0.0000000000e+00 3 5170 5.8027100000e-04 0 2092 0.0000000000e+00 2 74238 2.6940400000e-05 1 77776 1.2857400000e-05 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000265379.10:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 256076 NM_001278298.1:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 256076 NM_153264.6:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 256076 XM_011512621.2:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 256076 XM_011512622.2:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130413557 rs190283135 C T . PASS T stop_gained COL6A5 256076 XM_011512623.2:c.4675C>T 15 41342 3.6282700000e-04 0 3458 0.0000000000e+00 129 67724 1.9047900000e-03 1 10554 9.4750800000e-05 0 4788 0.0000000000e+00 56 15212 3.6813000000e-03 0 5182 0.0000000000e+00 8 2078 3.8498600000e-03 87 74022 1.1753300000e-03 122 77540 1.5733800000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 ENSG00000172752 ENST00000265379.10:c.4951-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 256076 NM_001278298.1:c.4951-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 256076 NM_153264.6:c.4951-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 256076 XM_011512621.2:c.4888-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 256076 XM_011512622.2:c.4951-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130421152 rs139339125 G T . PASS T splice_acceptor_variant COL6A5 256076 XM_011512623.2:c.4951-1G>T 2 41426 4.8278900000e-05 41 3470 1.1815600000e-02 39 67986 5.7364800000e-04 273 10600 2.5754700000e-02 1 4826 2.0721100000e-04 0 15242 0.0000000000e+00 10 5166 1.9357300000e-03 4 2094 1.9102200000e-03 245 74236 3.3002900000e-03 125 77802 1.6066400000e-03 chr3 130440486 rs2201717 C T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000265379.10:c.6136C>T 118 41434 2.8479000000e-03 0 3470 0.0000000000e+00 565 68014 8.3071100000e-03 224 10612 2.1108200000e-02 22 4834 4.5511000000e-03 952 15266 6.2360800000e-02 1 5190 1.9267800000e-04 26 2090 1.2440200000e-02 1011 74316 1.3604100000e-02 897 77822 1.1526300000e-02 chr3 130440486 rs2201717 C T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000512836.5:c.904C>T 118 41434 2.8479000000e-03 0 3470 0.0000000000e+00 565 68014 8.3071100000e-03 224 10612 2.1108200000e-02 22 4834 4.5511000000e-03 952 15266 6.2360800000e-02 1 5190 1.9267800000e-04 26 2090 1.2440200000e-02 1011 74316 1.3604100000e-02 897 77822 1.1526300000e-02 chr3 130440486 rs2201717 C T . PASS T stop_gained COL6A5 256076 NM_001278298.1:c.6148C>T 118 41434 2.8479000000e-03 0 3470 0.0000000000e+00 565 68014 8.3071100000e-03 224 10612 2.1108200000e-02 22 4834 4.5511000000e-03 952 15266 6.2360800000e-02 1 5190 1.9267800000e-04 26 2090 1.2440200000e-02 1011 74316 1.3604100000e-02 897 77822 1.1526300000e-02 chr3 130440486 rs2201717 C T . PASS T stop_gained COL6A5 256076 NM_153264.6:c.6148C>T 118 41434 2.8479000000e-03 0 3470 0.0000000000e+00 565 68014 8.3071100000e-03 224 10612 2.1108200000e-02 22 4834 4.5511000000e-03 952 15266 6.2360800000e-02 1 5190 1.9267800000e-04 26 2090 1.2440200000e-02 1011 74316 1.3604100000e-02 897 77822 1.1526300000e-02 chr3 130440486 rs2201717 C T . PASS T stop_gained COL6A5 256076 XM_011512621.2:c.6085C>T 118 41434 2.8479000000e-03 0 3470 0.0000000000e+00 565 68014 8.3071100000e-03 224 10612 2.1108200000e-02 22 4834 4.5511000000e-03 952 15266 6.2360800000e-02 1 5190 1.9267800000e-04 26 2090 1.2440200000e-02 1011 74316 1.3604100000e-02 897 77822 1.1526300000e-02 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000265379.10:c.6802G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000373157.8:c.643G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000512482.1:c.319G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 ENSG00000172752 ENST00000512836.5:c.1570G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 256076 NM_001278298.1:c.6814G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 256076 NM_153264.6:c.6814G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130468818 rs115375867 G T . PASS T stop_gained COL6A5 256076 XM_011512621.2:c.6751G>T 60 41434 1.4480900000e-03 41 3468 1.1822400000e-02 554 67964 8.1513700000e-03 71 10624 6.6829800000e-03 61 4828 1.2634600000e-02 27 15242 1.7714200000e-03 1 5168 1.9349800000e-04 12 2094 5.7306600000e-03 401 74264 5.3996600000e-03 426 77786 5.4765600000e-03 chr3 130471876 rs11355796 AT A . PASS - frameshift_variant COL6A5 ENSG00000172752 ENST00000265379.10:c.7760del 12200 41328 2.9519900000e-01 2570 3468 7.4106100000e-01 53731 67902 7.9130200000e-01 8220 10544 7.7959000000e-01 2923 4802 6.0870500000e-01 9794 15204 6.4417300000e-01 2173 5122 4.2424800000e-01 1323 2082 6.3544700000e-01 45762 74018 6.1825500000e-01 48085 77660 6.1917300000e-01 chr3 130471876 rs11355796 AT A . PASS - frameshift_variant COL6A5 256076 XM_011512621.2:c.7709del 12200 41328 2.9519900000e-01 2570 3468 7.4106100000e-01 53731 67902 7.9130200000e-01 8220 10544 7.7959000000e-01 2923 4802 6.0870500000e-01 9794 15204 6.4417300000e-01 2173 5122 4.2424800000e-01 1323 2082 6.3544700000e-01 45762 74018 6.1825500000e-01 48085 77660 6.1917300000e-01