TB-Profiler result

Run: SRR1181542
Summary

Run ID: SRR1181542

Sample name:

Date: 2024-10-05T11:38:30.545140

Number of reads: 22074

Percentage reads mapped: 0.57

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.53 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
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 1472106 n.261G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.78 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472215 n.370A>T non_coding_transcript_exon_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472226 n.381A>G non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472234 n.389T>A non_coding_transcript_exon_variant 0.36 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.53 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>A non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472244 n.399C>T non_coding_transcript_exon_variant 0.45 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.52 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472592 n.747C>T non_coding_transcript_exon_variant 0.44 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472735 n.890C>G non_coding_transcript_exon_variant 0.34 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472740 n.895G>C non_coding_transcript_exon_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.45 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472785 n.940G>A non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472805 n.960C>A non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473130 n.1285G>T non_coding_transcript_exon_variant 0.77 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473158 n.1313T>C non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.63 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>T non_coding_transcript_exon_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>C non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473200 n.1355_1357delAACinsCAT non_coding_transcript_exon_variant 0.54 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473200 n.1355A>C non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473204 n.1359C>G non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474165 n.508G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474171 n.514C>G non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474208 n.551C>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474213 n.556G>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.58 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 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476443 n.2786G>A non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476455 n.2798C>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.32 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 0.67 capreomycin Not assoc w R
linezolid Uncertain significance