TB-Profiler result

Run: SRR13837600
Summary

Run ID: SRR13837600

Sample name:

Date: 2024-10-04T11:43:16.241582

Number of reads: 2938966

Percentage reads mapped: 95.03

Median coverage: 99.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG c.926_927insA Assoc w R High-level resistance
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 2155185 c.926_927insA frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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 8396 p.Tyr365* stop_gained 1.0 levofloxacin
moxifloxacin
Rv0010c 13610 c.-52A>C upstream_gene_variant 1.0 isoniazid
fgd1 490821 p.Glu13Asp missense_variant 1.0 pretomanid
delamanid
clofazimine
mshA 575959 p.Gln204His missense_variant 1.0 isoniazid
ethionamide
rpoC 766364 p.Ala999Ser missense_variant 1.0 rifampicin
mmpL5 775945 p.Val846Leu missense_variant 1.0 bedaquiline
clofazimine
mmpL5 778345 p.Leu46Ile missense_variant 1.0 bedaquiline
clofazimine
mmpL5 778992 c.-512C>T upstream_gene_variant 1.0 bedaquiline
clofazimine
mmpR5 779231 p.Glu81Val missense_variant 1.0 bedaquiline
clofazimine
rplC 800526 c.-283G>T upstream_gene_variant 1.0 linezolid
fbiC 1303186 p.Tyr86His missense_variant 1.0 pretomanid
delamanid
clofazimine
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063272 c.1456delC frameshift_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2101749 p.Thr432Ser missense_variant 0.99 isoniazid
delamanid
ethionamide
katG 2155982 p.Asn44His missense_variant 1.0 isoniazid
PPE35 2168042 c.2571G>C synonymous_variant 1.0 pyrazinamide
PPE35 2169365 c.1248C>T synonymous_variant 1.0 pyrazinamide
Rv2477c 2784596 c.-554A>T upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067878 p.Val23Gly missense_variant 1.0 para-aminosalicylic_acid
fbiD 3339188 p.Thr24Ser missense_variant 1.0 pretomanid
delamanid
clofazimine
whiB7 3568496 p.Pro62Ser missense_variant 1.0 kanamycin
amikacin
streptomycin
Rv3236c 3612323 p.Pro265Gln missense_variant 1.0 pyrazinamide
fbiA 3641121 c.579C>A synonymous_variant 1.0 pretomanid
delamanid
clofazimine Not assoc w R - Interim
clpC1 4038346 p.Glu787* stop_gained 1.0 pyrazinamide
glpK 4139375 p.Asp127Glu missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4139545 p.Leu71Val missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4238896 c.-967C>A upstream_gene_variant 1.0 ethambutol
embC 4239894 p.Ala11Gly missense_variant 1.0 ethambutol
ethA 4327073 p.Leu134Pro missense_variant 1.0 ethionamide Uncertain significance