TB-Profiler result

Run: SRR18715333
Summary

Run ID: SRR18715333

Sample name:

Date: 2024-03-27T02:02:06.063166

Number of reads: 4700309

Percentage reads mapped: 99.2

Median coverage: 140.0

Strain: lineage2.2.1;lineage4.2.1.1

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
lineage2 East-Asian RD105 0.86
lineage4.2 Euro-American None 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.86
lineage4 Euro-American None 0.16
lineage4.2.1.1 Euro-American (TUR) None 0.15
lineage4.2.1 Euro-American (TUR) None 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. 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.Gly406Ser Assoc w R
pyrazinamide pncA p.Thr142Ala Assoc w R
p.Gly97Ser Assoc w R
p.Phe94Ser Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg 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
eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761110 p.Asp435Val missense_variant 0.12 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.16 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.18 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.15 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288818 p.Thr142Ala missense_variant 0.19 pyrazinamide Assoc w R
pncA 2288953 p.Gly97Ser missense_variant 0.28 pyrazinamide Assoc w R
pncA 2288961 p.Phe94Ser missense_variant 0.59 pyrazinamide Assoc w R - Interim
eis 2715342 c.-10G>A upstream_gene_variant 0.88 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247729 p.Gly406Ser missense_variant 0.16 ethambutol 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 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 0.88 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.87 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.86 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.89 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.9 ethionamide Uncertain significance
nusG 734624 p.Arg124Leu missense_variant 0.65 rifampicin Uncertain significance
rpoB 762286 p.Arg827Leu missense_variant 0.16 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 766376 p.Ile1003Val missense_variant 0.11 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.24 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 0.89 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.85 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776802 p.Met560Thr missense_variant 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777451 p.Val344Leu missense_variant 0.14 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.18 linezolid
Rv1129c 1254056 p.Asp160Ala missense_variant 0.25 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254131 p.Glu135Gly missense_variant 0.34 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.82 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.15 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472207 n.362A>T non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.81 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
bacA 2063685 c.1044G>A synonymous_variant 0.15 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.87 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.88 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.12 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065958 c.234G>A synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086731 c.-89A>G upstream_gene_variant 0.66 cycloserine
ald 3086742 c.-78A>C upstream_gene_variant 0.16 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87 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 0.83 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877956 p.Glu184Asp missense_variant 0.28 rifampicin Uncertain significance
ddn 3987092 p.Glu83Asp missense_variant 0.2 delamanid Uncertain significance
pretomanid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.14 ethambutol Uncertain significance
embA 4243346 c.114A>G synonymous_variant 0.58 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.23 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.79 ethambutol Not assoc w R
ethA 4327062 p.Ser138Arg missense_variant 0.25 ethionamide Uncertain significance
ethA 4327065 p.Cys137Arg missense_variant 0.54 ethionamide Uncertain significance
whiB6 4338371 p.Thr51Pro missense_variant 0.61 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 0.84 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.84 streptomycin Not assoc w R