TB-Profiler result

Run: SRR1180543
Summary

Run ID: SRR1180543

Sample name:

Date: 2024-05-17T14:44:51.858368

Number of reads: 16351

Percentage reads mapped: 0.55

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.88 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.82 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.56 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.54 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.33 kanamycin
amikacin
streptomycin Uncertain significance
capreomycin
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.34 kanamycin
amikacin
streptomycin Uncertain significance
capreomycin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.46 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.62 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472263 n.418C>T non_coding_transcript_exon_variant 0.54 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.66 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.55 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.84 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472592 n.747C>T non_coding_transcript_exon_variant 0.43 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.65 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.59 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.33 kanamycin
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.49 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472735 n.890C>G non_coding_transcript_exon_variant 0.22 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472742 n.897C>A non_coding_transcript_exon_variant 0.54 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.36 kanamycin
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472805 n.960C>A non_coding_transcript_exon_variant 0.26 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.26 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.31 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473158 n.1313T>C non_coding_transcript_exon_variant 0.42 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Not assoc w R
capreomycin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Not assoc w R
capreomycin Not assoc w R
rrs 1473177 n.1332G>T non_coding_transcript_exon_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473193 n.1348G>C non_coding_transcript_exon_variant 0.75 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473204 n.1359C>G non_coding_transcript_exon_variant 0.77 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476443 n.2786G>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476455 n.2798C>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>G non_coding_transcript_exon_variant 0.91 capreomycin
linezolid