TB-Profiler result

Run: ERR2516503
Summary

Run ID: ERR2516503

Sample name:

Date: 2024-10-05T12:32:16.713597

Number of reads: 2898212

Percentage reads mapped: 99.69

Median coverage: 59.0

Strain: lineage4

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
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 pncA p.Val180Gly Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala74Ser Uncertain significance Mutation from literature
p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala74Ser Uncertain significance Mutation from literature
p.Asp94Ala Assoc w R
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
gyrA 7521 p.Ala74Ser missense_variant 0.41 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Ala missense_variant 0.4 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288703 p.Val180Gly missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 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
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
mshA 575837 c.490C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575910 c.565delG frameshift_variant 0.98 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 575932 c.587dupC frameshift_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 766487 p.Pro1040Ala missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777875 c.605delG frameshift_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779181 c.198dupG frameshift_variant 0.98 bedaquiline Assoc w R
clofazimine Assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.98 linezolid Not assoc w R - Interim
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
ndh 2101831 c.1212G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 0.99 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726141 c.-52C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
thyA 3074495 c.-24C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv3083 3448679 c.177dupG frameshift_variant 0.46 ethionamide Uncertain significance
Rv3236c 3612219 p.Val300Ile missense_variant 1.0 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326632 p.His281Arg missense_variant 0.26 ethionamide Uncertain significance
ethA 4326771 p.Tyr235Asp missense_variant 0.54 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 1.0 ethionamide
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 4407967 p.Leu79Trp missense_variant 1.0 streptomycin Uncertain significance