TB-Profiler result

Run: SRR1180174
Summary

Run ID: SRR1180174

Sample name:

Date: 2024-03-26T16:46:49.928552

Number of reads: 22217

Percentage reads mapped: 0.6

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 rrs n.888G>A Uncertain significance Mutation from literature
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
amikacin 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 1472160 n.315C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472204 n.359G>A non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472215 n.370A>T non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472226 n.381A>G non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472234 n.389T>A non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>A non_coding_transcript_exon_variant 0.62 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472244 n.399C>T non_coding_transcript_exon_variant 0.62 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.93 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472264 n.419_420delTTinsCTA non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472735 n.890C>G non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472740 n.895G>C non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473158 n.1313T>C non_coding_transcript_exon_variant 0.78 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 1.0 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 1.0 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>C non_coding_transcript_exon_variant 0.89 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473204 n.1359C>G non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 1.0 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 1476313 n.2656G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476443 n.2786G>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476455 n.2798C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
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 0.54 capreomycin Not assoc w R
linezolid Uncertain significance