TB-Profiler result

Run: SRR13838014
Summary

Run ID: SRR13838014

Sample name:

Date: 2024-10-05T06:18:48.581535

Number of reads: 2938471

Percentage reads mapped: 98.01

Median coverage: 99.0

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
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Trp45* Assoc w R
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
ethA 4327340 p.Trp45* stop_gained 1.0 ethionamide Assoc w R
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
gyrA 8646 p.Gln449Lys missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9138 p.Gln613Lys missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9604 p.Val768Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13326 c.232delC frameshift_variant 1.0 isoniazid Uncertain significance
ccsA 619641 c.-250T>C upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
ccsA 620748 c.858T>G synonymous_variant 1.0 kanamycin
capreomycin
amikacin
Rv0565c 656228 p.Ala415Ser missense_variant 1.0 ethionamide
mmaA3 738274 c.-125A>T upstream_gene_variant 1.0 isoniazid
rpoB 761853 p.Ile683Val missense_variant 1.0 rifampicin
mmpL5 777509 c.972G>T synonymous_variant 1.0 bedaquiline
clofazimine
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0 bedaquiline
clofazimine
Rv1258c 1406904 c.436dupT frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11 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 0.14 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 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674552 c.351C>G synonymous_variant 1.0 isoniazid
ethionamide
rpsA 1834079 p.Arg180Cys missense_variant 1.0 pyrazinamide
bacA 2063798 p.Thr311Ser missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2168448 p.Gln722Pro missense_variant 1.0 pyrazinamide
Rv1979c 2221876 p.Val430Glu missense_variant 1.0 bedaquiline
clofazimine
kasA 2518036 c.-78delG upstream_gene_variant 1.0 isoniazid
kasA 2518088 c.-27T>A upstream_gene_variant 1.0 isoniazid
eis 2714449 p.Trp295Ser missense_variant 1.0 kanamycin
amikacin
eis 2714773 p.Pro187Gln missense_variant 1.0 kanamycin
amikacin
eis 2715525 c.-193G>T upstream_gene_variant 1.0 kanamycin
amikacin
ahpC 2726611 c.419_420insA frameshift_variant 1.0 isoniazid Uncertain significance
folC 2747455 c.144C>A synonymous_variant 1.0 para-aminosalicylic_acid
pepQ 2859723 c.696T>C synonymous_variant 0.99 bedaquiline
clofazimine Not assoc w R - Interim
ribD 2987540 c.702G>T synonymous_variant 1.0 para-aminosalicylic_acid
fbiD 3339321 c.204G>A synonymous_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4038436 p.Ala757Ser missense_variant 1.0 pyrazinamide
embC 4239186 c.-677A>C upstream_gene_variant 1.0 ethambutol
embC 4242635 p.Ala925Ser missense_variant 1.0 ethambutol
embB 4249145 c.2634delC frameshift_variant 1.0 ethambutol
ubiA 4269803 p.Ala11Pro missense_variant 1.0 ethambutol
ethA 4326689 p.Lys262Thr missense_variant 1.0 ethionamide
ethA 4326849 p.Pro209Thr missense_variant 1.0 ethionamide
whiB6 4338822 c.-301A>C upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin