TB-Profiler result

Run: ERR779903
Summary

Run ID: ERR779903

Sample name:

Date: 2024-04-16T07:39:28.496890

Number of reads: 4217201

Percentage reads mapped: 99.67

Median coverage: 90.0

Strain: lineage4.1.1;lineage4.3.4.2

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 0.46
lineage4.1 Euro-American None 0.57
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.56
lineage4.3.4 Euro-American (LAM) RD174 0.43
lineage4.3.4.2 Euro-American (LAM) RD174 0.45
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
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 761155 p.Ser450Leu missense_variant 0.39 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.36 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.43 ethambutol 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
gyrB 6052 p.Ile271Met missense_variant 0.63 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7221 p.Ser661Thr missense_variant 0.51 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 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.55 ethionamide Uncertain significance
rpoC 764918 p.Val517Leu missense_variant 0.47 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.59 rifampicin Not assoc w R
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
rplC 800219 c.-590T>C upstream_gene_variant 0.58 linezolid
embR 1416699 p.Leu217Val missense_variant 0.54 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673865 c.-337C>T upstream_gene_variant 0.54 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833469 c.-73G>T upstream_gene_variant 0.39 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995813 c.-292C>T upstream_gene_variant 0.54 capreomycin
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.48 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.46 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.43 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627511 c.-162C>G upstream_gene_variant 0.6 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.41 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.54 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.47 ethambutol Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4407970 p.Pro78Leu missense_variant 0.37 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.5 streptomycin Not assoc w R