TB-Profiler result

Run: SRR16915764
Summary

Run ID: SRR16915764

Sample name:

Date: 2024-04-15T03:53:07.728682

Number of reads: 32298429

Percentage reads mapped: 99.62

Median coverage: 845.0

Strain: lineage2.2.1;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 0.84
lineage2 East-Asian RD105 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.16
lineage4 Euro-American None 0.84
lineage4.3.4 Euro-American (LAM) RD174 0.84
lineage4.3.4.2 Euro-American (LAM) RD174 0.83
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 ethA c.752dupG 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 0.85 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.83 ethambutol Assoc w R
ethA 4326721 c.752dupG frameshift_variant 0.83 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
dnaA 64 p.Gly22Arg missense_variant 0.16 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7087 p.Met616Ile missense_variant 0.83 levofloxacin
moxifloxacin
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
fgd1 491742 c.960T>C synonymous_variant 0.16 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.17 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.16 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764918 p.Val517Leu missense_variant 0.83 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.82 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.19 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1406964 p.Ser126Trp missense_variant 0.16 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833469 c.-73G>T upstream_gene_variant 0.82 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
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 0.15 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
PPE35 2169750 p.Gly288Glu missense_variant 0.16 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995916 c.-189G>A upstream_gene_variant 0.17 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.82 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.17 streptomycin
amikacin
kanamycin
Rv3236c 3612009 p.Ala370Thr missense_variant 0.82 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.17 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.83 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.86 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 0.17 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.24 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.13 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.16 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.16 ethionamide Uncertain significance
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 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R
gid 4407970 p.Pro78Leu missense_variant 0.83 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.81 streptomycin Not assoc w R