TB-Profiler result

Run: SRR6824299

Summary

Run ID: SRR6824299

Sample name:

Date: 2024-10-04T23:47:26.010870

Number of reads: 17335192

Percentage reads mapped: 98.33

Median coverage: 505.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: MDR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.8
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.2
lineage2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage4 Euro-American None 0.81
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
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 0.22 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.21 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid Assoc w R High-level resistance
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 1163 p.Thr388Ile missense_variant 0.78 isoniazid Uncertain significance
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 7892 c.591G>A synonymous_variant 0.79 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 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.2 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.78 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.2 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.16 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.18 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.2 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 0.21 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.19 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpR5 779079 p.Arg30Ser missense_variant 0.81 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253900 p.Leu212Arg missense_variant 0.8 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302905 c.-26T>G upstream_gene_variant 0.21 pretomanid
delamanid
clofazimine
Rv1258c 1406101 p.Pro414Ser missense_variant 0.78 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476077 n.2420T>G non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
inhA 1673359 c.-843T>G upstream_gene_variant 0.81 isoniazid
ethionamide
inhA 1674210 c.9A>C synonymous_variant 0.17 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
rpsA 1834177 c.636A>C synonymous_variant 0.2 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 0.23 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.18 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.83 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
ald 3086788 c.-32T>C upstream_gene_variant 0.22 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 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 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841207 p.His72Tyr missense_variant 0.19 cycloserine
rpoA 3877482 c.1026C>T synonymous_variant 0.78 rifampicin Not assoc w R - Interim
rpoA 3878575 c.-68C>T upstream_gene_variant 0.87 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.8 pyrazinamide Not assoc w R
embC 4239468 c.-395C>T upstream_gene_variant 0.82 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.21 ethambutol Not assoc w R
embB 4247828 p.Ala439Thr missense_variant 0.82 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.18 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 0.15 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R