TB-Profiler result

Run: SRR6356944
Summary

Run ID: SRR6356944

Sample name:

Date: 2024-10-05T11:53:24.207843

Number of reads: 1917581

Percentage reads mapped: 99.7

Median coverage: 57.0

Strain: lineage4.3.3;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
lineage4.3 Euro-American (LAM) None 0.6
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.39
lineage4.3.3 Euro-American (LAM) RD115 0.63
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Phe Assoc w R
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
pyrazinamide
streptomycin gid p.Leu74* Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.695dupG Assoc w R
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
gyrA 7581 p.Asp94Asn missense_variant 0.43 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Phe missense_variant 0.4 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.36 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)
tlyA 1918631 c.695dupG frameshift_variant 0.65 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 0.49 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
gid 4407982 p.Leu74* stop_gained 0.57 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 7496 c.195C>G synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656595 c.875dupC frameshift_variant 0.39 ethionamide Uncertain significance
rpoB 760742 c.936G>A synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 765083 p.Arg572Cys missense_variant 0.69 rifampicin Uncertain significance
rpoC 765369 p.Thr667Met missense_variant 0.37 rifampicin Uncertain significance
rpoC 766608 p.Ile1080Thr missense_variant 0.49 rifampicin Uncertain significance
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
Rv1129c 1253737 p.Ser266Arg missense_variant 0.4 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254536 c.-2A>G upstream_gene_variant 0.56 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1303095 c.165G>A synonymous_variant 0.52 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.5 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.6 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155690 p.Leu141Ser missense_variant 0.52 isoniazid Uncertain significance
katG 2156196 c.-85C>T upstream_gene_variant 0.69 isoniazid Not assoc w R
PPE35 2169312 c.1298_1300delACA disruptive_inframe_deletion 0.67 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.62 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.62 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.65 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.57 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.63 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841362 p.Thr20Met missense_variant 0.64 cycloserine
alr 3841612 c.-193_-192insC upstream_gene_variant 0.36 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.73 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326450 p.Thr342Ala missense_variant 0.63 ethionamide 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
whiB6 4338732 c.-211C>T upstream_gene_variant 0.68 kanamycin
capreomycin
amikacin
gid 4407785 p.Ala140Pro missense_variant 0.38 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.73 streptomycin Not assoc w R