TB-Profiler result

Run: SRR13837925
Summary

Run ID: SRR13837925

Sample name:

Date: 2024-10-05T13:01:43.928887

Number of reads: 1469458

Percentage reads mapped: 96.02

Median coverage: 49.0

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 0.98 isoniazid
ethionamide
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 bedaquiline
clofazimine
mmpL5 776814 p.Gln556Arg missense_variant 1.0 bedaquiline
clofazimine
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 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1303535 p.Ser202Leu missense_variant 0.98 pretomanid
delamanid
clofazimine
Rv1258c 1407569 c.-229C>A upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
atpE 1461256 p.Met71Arg missense_variant 0.98 bedaquiline
rrs 1471638 n.-208T>C upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471836 n.-10A>G upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063043 c.1686T>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
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 bedaquiline
clofazimine
pncA 2289242 c.-1T>C upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2783664 c.378delA frameshift_variant 1.0 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol 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 rifampicin Uncertain significance
bedaquiline
mtrA 3627051 p.Asp100Val missense_variant 1.0 rifampicin
bedaquiline
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