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view test-data/sistr-results.tab @ 3:5c8ff92e38a9 draft

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Update to 1.0.2
author nml
date Wed, 14 Jun 2017 14:36:59 -0400
parents 13632190a0ff
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cgmlst_ST	cgmlst_distance	cgmlst_genome_match	cgmlst_matching_alleles	cgmlst_subspecies	fasta_filepath	genome	h1	h2	mash_distance	mash_genome	mash_match	mash_serovar	mash_subspecies	o_antigen	qc_messages	qc_status	serogroup	serovar	serovar_antigen	serovar_cgmlst
	0.8272727272727273	SAL_BA6036AA	57	enterica	/mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta	AE014613-699860	-	-	0.0637124	60369	151	Typhi		-	FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0	FAIL	-	-:-:-	-:-:-	Typhi