TB-Profiler result

Run: SRR29273928
Summary

Run ID: SRR29273928

Sample name:

Date: 2025-02-11T19:19:30.761317

Number of reads: 4787264

Percentage reads mapped: 99.7

Median coverage: 147.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-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
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
p.Ser450Leu Assoc w R
rpoC p.Gly332Arg Uncertain significance Mutation from literature
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
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Ala146Val Assoc w R
c.152dupA Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Gln125* Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asn499Lys Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Asn499Lys Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine alr p.Met343Thr Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1391dupA 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
gyrB 6736 p.Asn499Lys missense_variant 0.3 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Gly missense_variant 0.37 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Tyr missense_variant 0.31 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.71 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.64 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.5 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 1.0 isoniazid Assoc w R High-level resistance
pncA 2288805 p.Ala146Val missense_variant 0.68 pyrazinamide Assoc w R
pncA 2289089 c.152dupA frameshift_variant 0.37 pyrazinamide Assoc w R
alr 3840393 p.Met343Thr missense_variant 0.24 cycloserine Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.69 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.35 ethambutol Assoc w R
ethA 4326082 c.1391dupA frameshift_variant 0.64 ethionamide Assoc w R
gid 4407830 p.Gln125* stop_gained 0.67 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
dnaA 371 p.Pro124Leu missense_variant 0.68 isoniazid Not assoc w R
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.73 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9208 p.Lys636Thr missense_variant 0.36 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13543 p.Trp6Arg missense_variant 0.75 isoniazid Uncertain significance
Rv0010c 13624 c.-66C>T upstream_gene_variant 0.17 isoniazid Uncertain significance
rpoB 760295 p.Asn163Lys missense_variant 0.37 rifampicin Uncertain significance
rpoC 765008 p.Leu547Val missense_variant 0.67 rifampicin Uncertain significance
rpoC 766085 p.Pro906Ala missense_variant 0.65 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417985 c.-638C>A upstream_gene_variant 0.36 ethambutol
atpE 1460992 c.-53A>C upstream_gene_variant 0.64 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.38 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.22 capreomycin
Rv2752c 3066286 c.-95C>G upstream_gene_variant 0.33 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840489 p.Pro311Arg missense_variant 0.18 cycloserine
alr 3840764 c.657G>C synonymous_variant 0.7 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269311 p.Trp175Gly missense_variant 0.65 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R