TB-Profiler result

Run: ERR3509858
Summary

Run ID: ERR3509858

Sample name:

Date: 2024-10-05T01:49:00.450570

Number of reads: 4620875

Percentage reads mapped: 99.63

Median coverage: 121.0

Strain: lineage2.2.1;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 0.47
lineage2 East-Asian RD105 0.57
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.55
lineage2.2 East-Asian (Beijing) RD105;RD207 0.54
lineage4 Euro-American None 0.47
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.43
lineage4.3.4 Euro-American (LAM) RD174 0.44
lineage4.3.4.2 Euro-American (LAM) RD174 0.47
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
p.Asp94Gly Uncertain significance Mutation from literature
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Leu Assoc w R
p.Gly406Asp Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA c.419delG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.32delG 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.Ser450Leu missense_variant 0.59 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.34 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid Assoc w R High-level resistance
katG 2155831 p.Asp94Gly missense_variant 0.5 isoniazid Uncertain significance Mutation from literature
pncA 2288822 c.419delG frameshift_variant 0.55 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 0.43 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.44 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.35 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.12 ethambutol Assoc w R
ethA 4327441 c.32delG frameshift_variant 0.47 ethionamide 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 6140 p.Val301Leu missense_variant 0.39 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 8795 c.1494C>T synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.59 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.48 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.58 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.64 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 764703 p.Lys445Arg missense_variant 0.5 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.45 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.51 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779609 c.-704C>T upstream_gene_variant 0.44 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.57 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474982 n.1326dupA non_coding_transcript_exon_variant 0.51 capreomycin
linezolid Uncertain significance
inhA 1674429 c.228C>T synonymous_variant 0.45 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
rpsA 1834177 c.636A>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 0.56 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
katG 2154724 p.Arg463Leu missense_variant 0.55 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.55 pyrazinamide 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
pncA 2289909 c.-668G>A upstream_gene_variant 0.48 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.37 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.42 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.52 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.5 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.48 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.61 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.59 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 4407588 c.615A>G synonymous_variant 0.59 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.56 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R