TB-Profiler result

Run: SRR28394219
Summary

Run ID: SRR28394219

Sample name:

Date: 2024-05-22T08:25:05.710253

Number of reads: 6249815

Percentage reads mapped: 99.58

Median coverage: 178.0

Strain: lineage4.1.1.3;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 0.48
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.47
lineage4.1.1.3 Euro-American (X-type) RD193 0.5
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.55
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim 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 embB p.Ser297Ala Uncertain significance Mutation from literature
p.Gly406Ala Assoc w R
pyrazinamide pncA p.Thr135Pro Assoc w R
p.Trp119Cys Assoc w R - Interim
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
ethA c.1054delG Assoc w R
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.Ser450Trp missense_variant 0.51 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin Assoc w R
inhA 1674481 p.Ser94Ala missense_variant 0.52 isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
pncA 2288839 p.Thr135Pro missense_variant 0.45 pyrazinamide Assoc w R
pncA 2288885 p.Trp119Cys missense_variant 0.52 pyrazinamide Assoc w R - Interim
embB 4247402 p.Ser297Ala missense_variant 0.55 ethambutol Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.53 ethambutol Assoc w R
ethA 4326419 c.1054delG frameshift_variant 0.66 ethionamide Assoc w R
gid 4408100 c.102delG frameshift_variant 0.45 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
dnaA 808 p.Val270Ile missense_variant 0.28 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 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
Rv0010c 13452 p.Gly36Val missense_variant 0.53 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.47 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.52 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.44 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 766485 p.Val1039Gly missense_variant 0.48 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.42 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.54 linezolid
fbiC 1302954 c.24G>A synonymous_variant 0.46 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
embR 1416858 p.Thr164Ala missense_variant 0.37 ethambutol Uncertain significance
rrs 1471654 n.-192A>C upstream_gene_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674102 c.-100C>A upstream_gene_variant 0.4 ethionamide Uncertain significance
isoniazid 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
bacA 2062850 p.Trp627Arg missense_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2154678 c.1434G>C synonymous_variant 0.57 isoniazid Not assoc w R - Interim
PPE35 2169405 p.Asn403Ser missense_variant 0.61 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.44 isoniazid
ahpC 2726409 p.Asp73His missense_variant 0.62 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449437 c.936_942delCGCGGCG frameshift_variant 0.5 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626093 p.Gly174Ala missense_variant 0.48 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3841001 p.Glu140Asp missense_variant 0.6 cycloserine
glpK 4139183 c.572dupG frameshift_variant 0.51 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.48 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.49 ethambutol Not assoc w R
embB 4249678 c.3165C>A synonymous_variant 0.56 ethambutol Not assoc w R - Interim
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 4407934 p.Leu90Arg missense_variant 0.56 streptomycin Uncertain significance