TB-Profiler result

Run: SRR25827370
Summary

Run ID: SRR25827370

Sample name:

Date: 2024-10-04T14:05:12.323448

Number of reads: 8226015

Percentage reads mapped: 98.81

Median coverage: 274.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.66
lineage2 East-Asian RD105 0.37
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.32
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
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 embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA c.1290delC Assoc w R
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
delamanid
bedaquiline mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 0.48 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.27 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.32 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.35 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.37 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
thyA 3074408 p.Thr22Ala missense_variant 0.32 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.28 ethambutol Uncertain significance Mutation from literature
ethA 4326183 c.1290delC frameshift_variant 0.28 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Cys missense_variant 0.72 levofloxacin
moxifloxacin
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 13638 c.-80A>G upstream_gene_variant 0.31 isoniazid Uncertain significance
fgd1 491290 p.Val170Met missense_variant 0.47 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.33 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.37 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.34 ethionamide Uncertain significance
mmaA3 737899 p.Val84Gly missense_variant 0.65 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.65 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.59 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764703 p.Lys445Arg missense_variant 0.39 rifampicin Uncertain significance
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.32 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406221 p.Ala374Pro missense_variant 0.71 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833804 p.Ala88Gly missense_variant 0.66 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917670 c.-270G>A upstream_gene_variant 0.61 capreomycin
tlyA 1917851 c.-89C>A upstream_gene_variant 0.64 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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 2289047 c.195C>T synonymous_variant 0.64 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.63 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.66 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.62 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2783786 p.Arg86His missense_variant 0.66 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Not assoc w R
amikacin Uncertain significance
thyX 3067949 c.-4C>T upstream_gene_variant 0.5 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32 pyrazinamide Not assoc w R - Interim
Rv3236c 3613591 c.-475G>A upstream_gene_variant 0.71 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.34 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.63 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.32 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.64 ethambutol 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 0.35 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
embB 4247847 p.Gln445Arg missense_variant 0.22 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.22 ethambutol Not assoc w R
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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.36 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.37 streptomycin Not assoc w R