TB-Profiler result

Run: SRR29358136
Summary

Run ID: SRR29358136

Sample name:

Date: 2025-02-11T11:35:34.078588

Number of reads: 4768293

Percentage reads mapped: 99.58

Median coverage: 124.0

Strain: lineage4.1.1.3;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
lineage4.1 Euro-American None 0.75
lineage4.1.1.3 Euro-American (X-type) RD193 0.71
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.74
lineage4.9 Euro-American (H37Rv-like) None 0.26
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
gid c.386delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Pro224Leu Mutation from literature
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 1472359 n.514A>C non_coding_transcript_exon_variant 0.28 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.69 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid Assoc w R High-level resistance
ahpC 2726145 c.-48G>A upstream_gene_variant 0.24 isoniazid Uncertain significance Mutation from literature
thyX 3067961 c.-16C>T upstream_gene_variant 0.3 para-aminosalicylic_acid Mutation from literature
thyA 3073801 p.Pro224Leu missense_variant 0.29 para-aminosalicylic_acid Mutation from literature
gid 4407816 c.386delG frameshift_variant 0.35 streptomycin 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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.63 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.72 ethionamide Uncertain significance
hadA 732110 p.Cys61Gly missense_variant 0.36 isoniazid Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.79 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.79 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.73 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.68 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.73 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.69 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747453 p.Arg49Leu missense_variant 0.75 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.67 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.75 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.68 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.79 ethambutol Not assoc w R
ethA 4327240 c.234C>T synonymous_variant 0.71 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338719 c.-198T>C upstream_gene_variant 0.28 kanamycin
capreomycin
amikacin
whiB6 4338732 c.-211C>T upstream_gene_variant 0.73 kanamycin
capreomycin
amikacin
gid 4407839 p.Ser122Pro missense_variant 0.71 streptomycin Uncertain significance