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outputDescription.txt
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outputDescription.txt
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resistancePred.txt would include the following information:
----------------------------------------------
#Antibiotic resistance for ERR161312
********** List of presence genes: ***********
Exact gene matches:
chuU_CFT073:1.23|protMatch|NODE_6_length_203826_cov_33.5191_ID_20468|191041|192033|27.2505369529|5.46009656739,
chuX_CFT073:1.23|protMatch|NODE_6_length_203826_cov_33.5191_ID_20468|189875|190369|27.2505369529|5.46009656739,
cvaC_pAPECO2ColV:1.04|dnaMatch|NODE_44_length_11815_cov_28.3046_ID_20544|7314|7625|27.2505369529|5.46009656739,
Inexact matches: 65 (sequences with many mismatches likely having indels causing frameshift, or sequence where there are many Ns because it's too diverged from the reference sequence for the aligner to map to)
P3:None|mapBased|1.25|59.8492142857,99.54|G180R|,,piperacillin-tazobactam:S,co-amoxiclav:S,cephalexin:S,amoxicillin_ampicillin:R with non-IRT-TEM
TEM-1:None|mapBased|3.22415795587|59.8492142857,99.54|C721M:G421K:C228T:G396K|R241X:G141X,,ceftriaxone:S,amoxicillin_ampicillin:R,co-amoxiclav:S,aztreonam:S,cephalexin:R,cefepime:S,carbapenems:S,cefoxitin:S,ceftazidime:S,piperacillin-tazobactam:S,penicillin:R,cefuroxime:S
ampC:0.82|NODE_4_length_345437_cov_22.2442_ID_20464|11621|12187|27.2505369529|5.46009656739,97.62|C769T:T258G:T387C:T642C:G138A:C788T:G789A:G22A:G675A:A807G:A1068T:T687A:G946C:T57C:C571A:C60A:C1098T:G1099A:A1100C:C852T:C603T:T1119C:G1123A:A996G:C625T:G893T:G126C|L257F:T263I:A8T:S298I:D367T:P209S:A375T:A316P:Q191K,,penicillin:see promoter in for effect in combination with promoter mutations
********* Resistance prediction ********
chuU_CFT073, none, virulence factor:R
chuX_CFT073, none, virulence factor:R
cvaC_pAPECO2ColV, none, virulence factor:R
----------------------------------------------
For assembly based matching:
For exact matching:
geneName:copyNumber|matchingStatus|contig|startPos|endPost|meanCov|stdCov,resistanceProfile
where matchingStatus could be 'protMatch' or 'dnaMatch'
For inexact matching:
the closest allele is provided.
geneName:copyNumber|contig|startPos|endPos|meanCov|stdCov,percentIdentity|dnaMutation|proteinMutation, resistanceProfile
For mapBased matching:
Exact match gene:
geneName:copyNumber|mapBasedFlag|depthCov|meanDepthCovOfReferenceLoci, resistanceProfile
Inexact gene match:
geneName:copyNumber|mapBasedFlag|depthCov|meanDepthCovOfReferenceLoci,percentIdentity|dnaMutation|proteinMutation, resistanceProfile
Resistance prediction shows the mechanisms that can lead to the phenotypic prediction:
geneName, geneInCombination, resistance phenotype
where geneInCombination is another gene that is associated with the first gene in order to cause the resistance phenotype
or it could be the list of mutation that cause the resistance phenotype (for chromosomal genes or promoter SNPs, e.g. SNPS in the qrdr region of gyrA or in the ampC promoter region of ampC gene)
-----------------------------------------------------------
genotypePred.txt
resistType,ERR161312,chuU_CFT073,100.0,99.8,C261T|C207A,1.23,0,NODE_6_length_203826_cov_33.5191_ID_20468|191041|192033|27.2505369529|5.46009656739|protMatch
typingMethod,sampleName, gene, coverageLen,percentIdentity, dnaMutation, copyNumber, protein is truncated (0 means not, 1 means is truncated), comments
comments could contain either contig|start|end|meanCov|stdCov|matchStatus
or mapBased|depthCov|meanDepthCov
-----------------------------------------------------------
sampleStats.txt
Estimated number of samples: 1
Assembly size: 5498591
Mean contig coverage: 27.2505369529
Std contig coverage: 5.46009656739
Mean depth from BAM: 59.8492142857