TB-Profiler result

Run: SRR29093482
Summary

Run ID: SRR29093482

Sample name:

Date: 2024-10-04T04:51:29.306212

Number of reads: 3282520

Percentage reads mapped: 99.33

Median coverage: 112.0

Strain: lineage4.3.4.2.1

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 0.99
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.99
lineage4.3.4 Euro-American (LAM) RD174 0.98
lineage4.3.4.2 Euro-American (LAM) RD174 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid katG p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
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
rpoB 761139 p.His445Asp missense_variant 0.96 rifampicin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.96 streptomycin Uncertain significance Mutation from literature
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 769 p.Ala257Ser missense_variant 1.0 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin 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
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99 pyrazinamide Not assoc w R
lpqB 3623818 p.Gly365Arg missense_variant 1.0 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840706 p.Ala239Pro missense_variant 0.98 cycloserine
alr 3840719 c.702A>G synonymous_variant 0.99 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.99 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.99 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R