TB-Profiler result

Run: ERR4813384
Summary

Run ID: ERR4813384

Sample name:

Date: 2024-10-05T09:56:37.339500

Number of reads: 2080811

Percentage reads mapped: 99.56

Median coverage: 67.0

Strain: lineage4.1.1;lineage4.3.3

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 0.13
lineage4.1 Euro-American None 0.88
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.87
lineage4.3.3 Euro-American (LAM) RD115 0.15
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
pyrazinamide
streptomycin gid c.351dupG Assoc w R
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 0.16 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid Assoc w R High-level resistance
gid 4407851 c.351dupG frameshift_variant 0.77 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
gyrB 6052 p.Ile271Met missense_variant 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.81 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 8040 p.Gly247Ser missense_variant 0.17 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 0.78 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
rpoC 765639 p.Glu757Ala missense_variant 0.14 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
rplC 800219 c.-590T>C upstream_gene_variant 0.95 linezolid
embR 1416699 p.Leu217Val missense_variant 0.83 ethambutol Uncertain significance
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 1.0 capreomycin Not assoc w R
katG 2154459 c.1653C>T synonymous_variant 0.12 isoniazid Not assoc w R - Interim
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 0.16 isoniazid
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.89 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.16 para-aminosalicylic_acid
thyA 3074588 c.-117A>G upstream_gene_variant 0.88 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627511 c.-162C>G upstream_gene_variant 0.89 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.13 pyrazinamide Not assoc w R
panD 4044824 c.-543C>G upstream_gene_variant 0.17 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.84 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.84 ethambutol Not assoc w R
ethA 4326116 p.Thr453Ile missense_variant 0.93 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 1.0 kanamycin
capreomycin
amikacin
gid 4408003 p.Asp67Gly missense_variant 0.11 streptomycin Uncertain significance