TB-Profiler result

Run: SRR13232458
Summary

Run ID: SRR13232458

Sample name:

Date: 2024-04-15T12:34:18.828030

Number of reads: 2597709

Percentage reads mapped: 99.51

Median coverage: 71.0

Strain: lineage2.2.1;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 0.19
lineage2 East-Asian RD105 0.8
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.82
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.17
lineage4.3.3 Euro-American (LAM) RD115 0.14
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.Met306Val Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide pncA p.Ile31Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.341delA 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 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.77 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289150 p.Ile31Ser missense_variant 0.77 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.24 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.74 ethambutol Assoc w R
ethA 4327132 c.341delA 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
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 8040 p.Gly247Ser missense_variant 0.21 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 13287 p.Glu91Gly missense_variant 0.83 isoniazid
Rv0010c 13471 p.Leu30Val missense_variant 0.18 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.82 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.89 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.85 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
hadA 731688 c.-242C>T upstream_gene_variant 0.18 isoniazid
rpoB 762477 p.Lys891Glu missense_variant 0.87 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.72 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.12 rifampicin Uncertain significance
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 0.86 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83 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 0.89 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1365139 p.His243Tyr missense_variant 0.13 pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674305 p.Gln35Arg missense_variant 0.29 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.8 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.19 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 0.86 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.21 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.19 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.22 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 0.88 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.15 para-aminosalicylic_acid
ald 3086731 c.-89A>G upstream_gene_variant 0.82 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73 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 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.14 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.88 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.77 ethambutol Not assoc w R
embA 4244138 c.906G>A synonymous_variant 0.81 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.78 ethambutol Not assoc w R
ethA 4326299 p.Thr392Arg missense_variant 0.24 ethionamide Uncertain significance
whiB6 4338371 p.Thr51Pro missense_variant 0.81 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 0.89 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.76 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.17 streptomycin Not assoc w R