annotate test-data/amr_mutation_regions.bed @ 17:eb86b4bf140e draft default tip

Uploaded

1 #contig	start	stop	name	type	drug	note
2 chromosome	6843	6862	gyrA QRDR	snp	quinolone	gyrA QRDR mutation is the most common quinolone resistance mutation.  It has not been observed in naturally occuring isolates.
3 chromosome	5664	6166	gyrB QRDR	snp	quinolone	gyrB QRDR mutation is less a less common quinolone resistance mutation.  It has not been observed in naturally occuring isolates.
4 chromosome	124092	124443	rplV	any	macrolide	rplV alteration has been associated with macrolide resistance.
5 chromosome	3365449	3365459	parC QRDR 1	snp	quinolone	parC QRDR mutation is less a less common quinolone resistance mutation.  It has not been observed in naturally occuring isolates.   
6 chromosome	3365231	3365648	parC QRDR 2	snp	quinolone	parC QRDR mutation is less a less common quinolone resistance mutation.  It has not been observed in naturally occuring isolates.   
7 chromosome	3366159	3366605	parE QRDR 	snp	quinolone	parE QRDR mutation is less a less common quinolone resistance mutation.  It has not been observed in naturally occuring isolates.   
8 chromosome	842403	842981	tetR	any	quinolone	terR inactivation has been shown to confer quinolone resistance in a lab setting.  It has not been observed in natually ocurring isolates.
9 chromosome	2323274	2323294	rsip poly-A	any	beta-lactam	 rsiP inactivation has been shown to confer penicillin resistance in a lab setting.  It has not been observed in naturally ocurring isolates.
10 chromosome	2323269	2324096	rsip broad-gene	any	beta-lactam	 rsiP inactivation has been shown to confer penicillin resistance in a lab setting.  It has not been observed in naturally ocurring isolates.
11 chromosome	2421872	2421877	abc-f poly-A	indel	lincosamide	 Restoration of the abc-f ORF has been associated with lincosamide resistance in a lab setting.  It has not been observed in naturally ocurring isolates.
12 chromosome	9307	10861	16S.1	point	NA	NA
13 chromosome	11230	14158	23S.1	point	NA	NA
14 chromosome	14203	14318	5S.1	point	NA	NA
15 chromosome	29101	30655	16S.2	point	NA	NA
16 chromosome	31024	33952	23S.2	point	NA	NA
17 chromosome	33997	34112	5S.2	point	NA	NA
18 chromosome	82423	83977	16S.3	point	NA	NA
19 chromosome	84119	87047	23S.3	point	NA	NA
20 chromosome	87093	87208	5S.3	point	NA	NA
21 chromosome	145487	147041	16S.4	point	NA	NA
22 chromosome	147183	150111	23S.4	point	NA	NA
23 chromosome	150194	150309	5S.4	point	NA	NA
24 chromosome	246207	247761	16S.5	point	NA	NA
25 chromosome	247903	250831	23S.5	point	NA	NA
26 chromosome	250877	250992	5S.5	point	NA	NA
27 chromosome	266786	268340	16S.6	point	NA	NA
28 chromosome	268482	271410	23S.6	point	NA	NA
29 chromosome	271456	271571	5S.6	point	NA	NA
30 chromosome	280084	281638	16S.7	point	NA	NA
31 chromosome	281780	284708	23S.7	point	NA	NA
32 chromosome	284755	284870	5S.7	point	NA	NA
33 chromosome	290057	291611	16S.8	point	NA	NA
34 chromosome	291753	294681	23S.8	point	NA	NA
35 chromosome	294728	294843	5S.8	point	NA	NA
36 chromosome	532435	533988	16S.9	point	NA	NA
37 chromosome	534123	537051	23S.9	point	NA	NA
38 chromosome	537148	537263	5S.9	point	NA	NA
39 chromosome	741537	743091	16S.10	point	NA	NA
40 chromosome	743233	746161	23S.10	point	NA	NA
41 chromosome	746259	746374	5S.10	point	NA	NA
42 chromosome	4652034	4652149	5S.11	point	NA	NA
43 chromosome	4652247	4655175	23S.11	point	NA	NA
44 chromosome	4655317	4656870	16S.11	point	NA	NA