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annotate test-data/sistr-results.tabular @ 4:17fcac7ddf54 draft

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"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
author nml
date Thu, 06 Aug 2020 11:48:49 -0400
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17fcac7ddf54 "planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
nml
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1 cgmlst_ST cgmlst_distance cgmlst_found_loci 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
17fcac7ddf54 "planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
nml
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2 0.8272727272727273 58 2014-LET-0419 57 enterica /galaxy/database/files/000/dataset_695.dat AE014613-699860 - - 1.0 0 - 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. | INFO: Number of cgMLST330 loci found (n=58) | 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