TB-Profiler result

Run: SRR6356992
Summary

Run ID: SRR6356992

Sample name:

Date: 2024-04-15T12:57:35.610188

Number of reads: 2947004

Percentage reads mapped: 99.72

Median coverage: 90.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: MDR-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 0.62
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.38
lineage4.3.3 Euro-American (LAM) RD115 0.58
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
ofloxacin
levofloxacin
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
rpoB 761109 p.Asp435Phe missense_variant 0.3 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.43 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 0.44 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 0.34 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
gid 4407982 p.Leu74* stop_gained 0.61 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 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7581 p.Asp94Ser missense_variant 0.55 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656595 c.875dupC frameshift_variant 0.22 ethionamide Uncertain significance
rpoB 760742 c.936G>A synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.61 rifampicin Not assoc w R
rpoC 765083 p.Arg572Cys missense_variant 0.63 rifampicin Uncertain significance
rpoC 765369 p.Thr667Met missense_variant 0.4 rifampicin Uncertain significance
rpoC 766608 p.Ile1080Thr missense_variant 0.44 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253737 p.Ser266Arg missense_variant 0.33 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254536 c.-2A>G upstream_gene_variant 0.64 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1303095 c.165G>A synonymous_variant 0.47 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.74 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.61 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 0.36 isoniazid Uncertain significance
katG 2156196 c.-85C>T upstream_gene_variant 0.62 isoniazid Not assoc w R
PPE35 2169312 c.1298_1300delACA disruptive_inframe_deletion 0.36 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.56 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.55 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.62 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.7 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.64 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841362 p.Thr20Met missense_variant 0.61 cycloserine
alr 3841612 c.-193_-192insC upstream_gene_variant 0.43 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.6 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326450 p.Thr342Ala missense_variant 0.66 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.6 capreomycin
amikacin
kanamycin
gid 4407785 p.Ala140Pro missense_variant 0.38 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.58 streptomycin Not assoc w R