TB-Profiler result

Run: SRR13837927
Summary

Run ID: SRR13837927

Sample name:

Date: 2024-04-15T22:29:27.561797

Number of reads: 1469206

Percentage reads mapped: 99.0

Median coverage: 50.0

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.277G>C Mutation from literature
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
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 1.0 streptomycin 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
gyrB 5319 p.Arg27Leu missense_variant 1.0 levofloxacin
moxifloxacin
mshA 575032 c.-316A>G upstream_gene_variant 1.0 ethionamide
isoniazid
rpoB 760867 p.Gly354Asp missense_variant 1.0 rifampicin
rpoB 762496 c.2691delC frameshift_variant 1.0 rifampicin
rpoC 764793 p.Met475Arg missense_variant 1.0 rifampicin
rpoC 766563 p.Thr1065Ser missense_variant 1.0 rifampicin
mmpL5 775976 c.2505G>C synonymous_variant 1.0 clofazimine
bedaquiline
mmpL5 776814 p.Gln556Arg missense_variant 1.0 clofazimine
bedaquiline
rplC 800623 c.-186A>C upstream_gene_variant 1.0 linezolid
rplC 800769 c.-40A>T upstream_gene_variant 1.0 linezolid
Rv1129c 1253289 c.1246C>T synonymous_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1303535 p.Ser202Leu missense_variant 1.0 clofazimine
pretomanid
delamanid
Rv1258c 1407569 c.-229C>A upstream_gene_variant 1.0 streptomycin
isoniazid
pyrazinamide
atpE 1461256 p.Met71Arg missense_variant 1.0 bedaquiline
rrs 1471638 n.-208T>C upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471836 n.-10A>G upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063043 c.1686T>A synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2156157 c.-46C>A upstream_gene_variant 1.0 isoniazid
PPE35 2168627 p.Ile662Met missense_variant 1.0 pyrazinamide
Rv1979c 2222100 c.1065T>A synonymous_variant 1.0 clofazimine
bedaquiline
pncA 2289242 c.-1T>C upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2783664 c.378delA frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ribD 2987205 p.Ser123Ala missense_variant 1.0 para-aminosalicylic_acid
ribD 2987347 p.Pro170Leu missense_variant 1.0 para-aminosalicylic_acid
Rv2680 2995859 c.-246C>A upstream_gene_variant 1.0 capreomycin
Rv2681 2997492 p.Val252Phe missense_variant 1.0 capreomycin
Rv3083 3448903 p.Asp134His missense_variant 1.0 ethionamide
lpqB 3624372 p.Val180Ala missense_variant 1.0 bedaquiline
rifampicin Uncertain significance
mtrA 3627051 p.Asp100Val missense_variant 1.0 bedaquiline
rifampicin
clpC1 4039663 p.Gly348Ser missense_variant 1.0 pyrazinamide
embC 4241256 p.Arg465Thr missense_variant 1.0 ethambutol Uncertain significance
embA 4246449 p.Val1073Phe missense_variant 1.0 ethambutol
aftB 4268192 c.645G>C synonymous_variant 1.0 ethambutol