Commit 5751d0ab authored by Andreas Tille's avatar Andreas Tille
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New upstream version 1.0.0

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.coveragerc

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[run]

source = kleborate

Kleborate_results.txt

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strain	species	species_match	contig_count	N50	largest_contig	ST	virulence_score	resistance_score	num_resistance_classes	num_resistance_genes	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	rmpA	rmpA2	wzi	K_locus	K_locus_problems	K_locus_confidence	K_locus_identity	K_locus_missing_genes	O_locus	O_locus_problems	O_locus_confidence	O_locus_identity	O_locus_missing_genes	Chr_ST	gapA	infB	mdh	pgi	phoE	rpoB	tonB	ybtS	ybtX	ybtQ	ybtP	ybtA	irp2	irp1	ybtU	ybtT	ybtE	fyuA	clbA	clbB	clbC	clbD	clbE	clbF	clbG	clbH	clbI	clbL	clbM	clbN	clbO	clbP	clbQ	AGly	Col	Fcyn	Flq	Gly	MLS	Ntmdz	Phe	Rif	Sul	Tet	Tmt	Bla	Bla_Carb	Bla_ESBL	Bla_ESBL_inhR	Bla_broad	Bla_broad_inhR

Klebs_HS11286	Klebsiella pneumoniae	strong	7	5333942	5333942	ST11	1	2	9	17	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	-	wzi74	KL103	*	Very high	96.69%		O2v1	none	Very high	97.72%		ST11	3	3	1	1	1	1	4	14	11	14	5	9	22	19	10	5	11	11	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	StrB;StrA*;AadA2*;RmtB;Aac3-IId*?	-	-	GyrA-83I;ParC-80I	-	-	-	-	-	SulII	TetG	DfrA12?	AmpH*	KPC-2	CTX-M-14;CTX-M-14	-	SHV-11	TEM-30*;TEM-30*;TEM-30*

MGH78578	Klebsiella pneumoniae	strong	6	5315120	5315120	ST38	0	1	7	15	-	0	-	0	-	0	-	0	-	-	wzi50	KL52	none	Perfect	100.00%		OL101	*	High	94.91%		ST38	2	1	2	1	2	2	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	AadA1-pm*?;Aac6-Ib;StrB;Aph3''Ia;StrA;AadB	-	-	GyrA-83Y	-	-	-	CmlA5;CatA1*	-	SulI;SulII	TetD	-	AmpH*;SHV-187*;OXA-9*	-	SHV-12	-	-	TEM-54*;TEM-30*

NTUH-K2044	Klebsiella pneumoniae	strong	2	5248520	5248520	ST23	4	0	0	0	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 3	18-1LV	rmpA_11 (ICEKp1),rmpA_2 (KpVP-1)	rmpA2_3	wzi1	KL1	none	Perfect	100.00%		O1v2	none	Very high	99.13%		ST23	2	1	1	1	9	4	12	9	7	9	6	5	1	1	6	7	7	6	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	AmpH;SHV-190*	-	-	-	-	-

SGH10	Klebsiella pneumoniae	strong	2	5485114	5485114	ST23	5	0	0	0	ybt 1; ICEKp10	53	clb 2	29	iuc 1	1	iro 1	2	rmpA_2 (KpVP-1)	rmpA2_6*	wzi1	KL1	none	Very high	100.00%		O1v2	none	Very high	99.11%		ST23	2	1	1	1	9	4	12	2	2	2	2	2	6	124	2	2	2	2	2	2	2	2	2	2	2	3	2	2	2	2	2	2	2	-	-	-	-	-	-	-	-	-	-	-	-	AmpH;SHV-190*	-	-	-	-	-

README.md

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data/Genotyped_Isolates_Lam2017.txt

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data/README.md

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# Kleborate data



* [ncbi_genome_kleborate_results.txt](ncbi_genome_kleborate_results.txt) 

Kleborate output for all _Klebsiella_ genomes in NCBI (genomes downloaded using [this tool](https://github.com/kblin/ncbi-genome-download)). The first 21 columns in the file are NCBI's metadata for the genome. The remaining columns are Kleborate's output.



* [Genotyped_Isolates_Lam2017.txt](Genotyped_Isolates_Lam2017.txt)

Manually curated genotype information used in the Lam et al 2017 preprint



* [UK-IRE-MDR_Lam2017.txt](UK-IRE-MDR_Lam2017.txt)

Kleborate results for 200 MDR isolates from UK & Ireland [Moradigaravand et al, MBio 2017](http://mbio.asm.org/content/8/1/e01976-16.long) as reported in the Lam et al 2017 preprint