Mercurial > repos > iuc > snpeff

annotate test-data/pBR322.gff3 @ 29:ca2b512e8d7c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author iuc
date Mon, 21 Oct 2024 13:56:15 +0000
parents cfcf33df7fc0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
cfcf33df7fc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4366b6a23223f84039a0590cf0d7079b83d8f84"
iuc
parents: 15
diff changeset
1 ##gff-version 3
15
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
2 ##sequence-region J01749.1 1 4361
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
3 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=47470
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
4 J01749.1 Genbank region 1 4361 . + . ID=id-1;Dbxref=taxon:47470;Is_circular=true;gbkey=Src;mol_type=other DNA;tissue-lib=ATCC 31344%2C ATCC 37017
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
5 J01749.1 Genbank region 1 1762 . + . ID=id-J01749.1:1..1762;gbkey=Src
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
6 J01749.1 Genbank binding_site 24 27 . + . ID=id-J01749.1:24..27;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
7 J01749.1 Genbank promoter 27 33 . - . ID=id-J01749.1:27..33;Note=promoter P1 (6);gbkey=promoter
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
8 J01749.1 Genbank binding_site 39 42 . + . ID=id-J01749.1:39..42;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
9 J01749.1 Genbank promoter 43 49 . + . ID=id-J01749.1:43..49;Note=promoter P2 (6);gbkey=promoter
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
10 J01749.1 Genbank binding_site 53 56 . + . ID=id-J01749.1:53..56;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
11 J01749.1 Genbank binding_site 67 70 . + . ID=id-J01749.1:67..70;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
12 J01749.1 Genbank binding_site 80 83 . + . ID=id-J01749.1:80..83;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
13 J01749.1 Genbank gene 86 1276 . + . ID=gene-tet;Name=tet;gbkey=Gene;gene=tet
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
14 J01749.1 Genbank CDS 86 1276 . + 0 ID=cds-AAB59735.1;Parent=gene-tet;Dbxref=NCBI_GP:AAB59735.1;Name=AAB59735.1;gbkey=CDS;gene=tet;product=tetracycline resistance protein;protein_id=AAB59735.1;transl_table=11
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
15 J01749.1 Genbank binding_site 411 414 . + . ID=id-tet;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
16 J01749.1 Genbank binding_site 469 472 . + . ID=id-tet-2;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
17 J01749.1 Genbank sequence_difference 426 426 . + . ID=id-tet-3;Note=conflict;gbkey=misc_difference;gene=tet;replace=
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
18 J01749.1 Genbank sequence_feature 146 147 . + . ID=id-tet-4;Note=Endo.Sce I cleavage site coordinated with site at base 142 (10);gbkey=misc_feature;gene=tet
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
19 J01749.1 Genbank region 526 528 . + . ID=id-tet-5;gbkey=old_sequence;gene=tet
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
20 J01749.1 Genbank sequence_feature 141 142 . - . ID=id-J01749.1:141..142;Note=Endo.Sce I cleavage site coordinated with site at base 146 (10);gbkey=misc_feature
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
21 J01749.1 Genbank direct_repeat 1515 1519 . - . ID=id-J01749.1:1515..1519;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
22 J01749.1 Genbank sequence_feature 1636 1762 . + . ID=id-J01749.1:1636..1762;Note=from pSC101 (bp 1860-1986);gbkey=misc_feature
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
23 J01749.1 Genbank direct_repeat 1788 1792 . - . ID=id-J01749.1:1788..1792;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
24 J01749.1 Genbank sequence_difference 1891 1892 . + . ID=id-J01749.1:1891..1892;Note=conflict;gbkey=misc_difference;replace=att
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
25 J01749.1 Genbank region 1892 1893 . + . ID=id-J01749.1:1892..1893;gbkey=old_sequence
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
26 J01749.1 Genbank region 1905 1910 . + . ID=id-J01749.1:1905..1910;gbkey=RBS
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
27 J01749.1 Genbank region 1905 1909 . + . ID=id-J01749.1:1905..1909;Note=Shine-Dalgarno sequence;gbkey=RBS
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
28 J01749.1 Genbank sequence_difference 1913 1914 . + . ID=id-J01749.1:1913..1914;Note=conflict;gbkey=misc_difference;replace=caa
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
29 J01749.1 Genbank region 1914 1915 . + . ID=id-J01749.1:1914..1915;gbkey=old_sequence
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
30 J01749.1 Genbank CDS 1915 2106 . + 0 ID=cds-AAB59736.1;Dbxref=NCBI_GP:AAB59736.1;Name=AAB59736.1;gbkey=CDS;product=ROP protein;protein_id=AAB59736.1;transl_table=11
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
31 J01749.1 Genbank sequence_feature 2011 2167 . + . ID=id-J01749.1:2011..2167;Note=H-strand Y effector site;gbkey=misc_feature
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
32 J01749.1 Genbank direct_repeat 2245 2249 . - . ID=id-J01749.1:2245..2249;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
33 J01749.1 Genbank sequence_feature 2351 2414 . - . ID=id-J01749.1:2351..2414;Note=L-strand Y effector site;gbkey=misc_feature
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
34 J01749.1 Genbank binding_site 2439 2447 . + . ID=id-J01749.1:2439..2447;bound_moiety=dnaA;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
35 J01749.1 Genbank origin_of_replication 2535 2535 . + . ID=id-J01749.1:2535..2535;gbkey=rep_origin
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
36 J01749.1 Genbank region 2729 2730 . + . ID=id-J01749.1:2729..2730;Note=revision according to (17);gbkey=old_sequence;replace=at
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
37 J01749.1 Genbank region 2729 2729 . + . ID=id-J01749.1:2729..2729;gbkey=old_sequence
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
38 J01749.1 Genbank region 2730 2730 . + . ID=id-J01749.1:2730..2730;Note=revision according to (16);gbkey=old_sequence;replace=t
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
39 J01749.1 Genbank mobile_genetic_element 3148 4361 . + . ID=id-J01749.1:3148..4361;gbkey=mobile_element;mobile_element_type=transposon:Tn3
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
40 J01749.1 Genbank inverted_repeat 3148 3185 . + . ID=id-J01749.1:3148..3185;Note=corresponds to one of the 38bp repeats found in Tn3 (bp 1-38 and complement (4920-4957));gbkey=repeat_region;rpt_type=inverted
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
41 J01749.1 Genbank gene 3293 4153 . - . ID=gene-bla;Name=bla;gbkey=Gene;gene=bla
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
42 J01749.1 Genbank CDS 3293 4153 . - 0 ID=cds-AAB59737.1;Parent=gene-bla;Dbxref=NCBI_GP:AAB59737.1;Name=AAB59737.1;Note=E-286;gbkey=CDS;gene=bla;product=beta-lactamase;protein_id=AAB59737.1;transl_table=11
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
43 J01749.1 Genbank region 4161 4165 . - . ID=id-J01749.1:4161..4165;Note=Shine-Dalgarno sequence;gbkey=RBS
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
44 J01749.1 Genbank promoter 4188 4194 . - . ID=id-J01749.1:4188..4194;Note=promoter P3 (6);gbkey=promoter
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
45 J01749.1 Genbank binding_site 4268 4271 . - . ID=id-J01749.1:4268..4271;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
46 J01749.1 Genbank binding_site 4280 4283 . - . ID=id-J01749.1:4280..4283;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
47 J01749.1 Genbank binding_site 4285 4288 . - . ID=id-J01749.1:4285..4288;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
48 J01749.1 Genbank binding_site 4296 4299 . - . ID=id-J01749.1:4296..4299;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
49 J01749.1 Genbank binding_site 4311 4314 . - . ID=id-J01749.1:4311..4314;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
50 J01749.1 Genbank binding_site 4317 4320 . - . ID=id-J01749.1:4317..4320;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
51 J01749.1 Genbank binding_site 4331 4334 . - . ID=id-J01749.1:4331..4334;bound_moiety=echinomycin;gbkey=misc_binding
479c4f2f4826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
iuc
parents:
diff changeset
52