TB-Profiler result

Run: SRR25827747
Summary

Run ID: SRR25827747

Sample name:

Date: 2024-04-14T23:10:31.309154

Number of reads: 7265335

Percentage reads mapped: 99.24

Median coverage: 249.0

Strain: lineage2.2.1;lineage3.1.2

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.64
lineage3.1.2 East-African-Indian RD750 0.66
lineage2 East-Asian RD105 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.32
lineage3.1 East-African-Indian RD750 0.63
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.-12C>T Uncertain significance Mutation from literature
embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Lys96Thr Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1034delA Assoc w R
clofazimine mmpR5 p.Gln115* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Gln115* 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
gyrA 7582 p.Asp94Gly missense_variant 0.36 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.38 rifampicin Assoc w R
mmpR5 779332 p.Gln115* stop_gained 0.35 clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.38 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288955 p.Lys96Thr missense_variant 0.43 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.34 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.34 ethambutol Assoc w R
ethA 4326439 c.1034delA frameshift_variant 0.39 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 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 13628 c.-71delT upstream_gene_variant 0.34 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.31 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.37 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.29 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.66 rifampicin Not assoc w R
rpoB 761946 c.2140C>T synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.39 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 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 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303326 c.396C>T synonymous_variant 0.32 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406242 p.Ala367Thr missense_variant 0.63 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.39 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
tlyA 1918104 c.165G>A synonymous_variant 0.68 capreomycin Not assoc w R - Interim
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
PPE35 2168604 p.Pro670Leu missense_variant 0.69 pyrazinamide Not assoc w R
Rv1979c 2222357 p.Thr270Ala missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.6 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.65 pyrazinamide
eis 2715444 c.-112T>C upstream_gene_variant 0.64 amikacin
kanamycin
ahpC 2726105 c.-88G>A upstream_gene_variant 0.63 isoniazid Not assoc w R
folC 2747481 p.Glu40Lys missense_variant 0.35 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.67 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31 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 0.4 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840357 c.1061_1063delCGC disruptive_inframe_deletion 0.34 cycloserine
alr 3840876 p.Ala182Val missense_variant 0.67 cycloserine
alr 3841362 p.Thr20Met missense_variant 0.37 cycloserine
rpoA 3877960 p.Val183Gly missense_variant 0.36 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.62 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.63 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.61 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 0.39 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.15 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.32 ethambutol Not assoc w R
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 1.0 streptomycin Not assoc w R
gid 4407916 p.Arg96Leu missense_variant 0.61 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.39 streptomycin Not assoc w R