TB-Profiler result

Run: SRR1049023
Summary

Run ID: SRR1049023

Sample name:

Date: 2024-04-15T19:30:04.594493

Number of reads: 132184

Percentage reads mapped: 4.34

Median coverage: 2.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.94
lineage4.9 Euro-American (H37Rv-like) None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.421_423delTTGinsCC Assoc w R High-level resistance
p.Ser140Asn Uncertain significance Mutation from literature
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
katG 2155689 c.421_423delTTGinsCC frameshift_variant&missense_variant 0.76 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.72 isoniazid 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
rpoC 762965 c.-405T>C upstream_gene_variant 0.75 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.67 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.6 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.55 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.55 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.55 rifampicin
rpoC 764398 c.1029G>C synonymous_variant 0.55 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.6 rifampicin
rpoC 764410 c.1041G>T synonymous_variant 0.6 rifampicin
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
katG 2155613 p.Phe167Leu missense_variant 0.8 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.8 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.8 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.91 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.91 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.91 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.77 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.77 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.79 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.83 isoniazid
katG 2155704 c.408C>T synonymous_variant 0.75 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.7 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.68 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.68 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.68 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.68 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.65 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.65 isoniazid
katG 2155765 p.His116Thr missense_variant 0.57 isoniazid