TB-Profiler result

Run: SRR6824668
Summary

Run ID: SRR6824668

Sample name:

Date: 2024-10-05T06:32:11.552300

Number of reads: 9055048

Percentage reads mapped: 99.44

Median coverage: 272.0

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 0.74
lineage2 East-Asian RD105 0.25
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.25
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage4 Euro-American None 0.75
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Cys Assoc w R
isoniazid katG p.Thr275Pro Uncertain significance Mutation from literature
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
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 761139 p.His445Cys missense_variant 0.77 rifampicin Assoc w R
katG 2155289 p.Thr275Pro missense_variant 0.76 isoniazid Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 0.74 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.75 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
dnaA 435 c.435C>T synonymous_variant 0.78 isoniazid
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 0.73 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
Rv0010c 13155 p.Tyr135Cys missense_variant 0.77 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.23 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574620 c.-728C>T upstream_gene_variant 0.14 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.23 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619950 c.60G>C synonymous_variant 0.13 kanamycin
capreomycin
amikacin
ccsA 620029 c.139C>T synonymous_variant 0.76 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.25 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
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 0.19 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.21 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781676 c.117C>T synonymous_variant 0.79 streptomycin Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.29 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 0.25 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.23 pyrazinamide Not assoc w R
PPE35 2168862 p.Leu584Gln missense_variant 0.15 pyrazinamide
PPE35 2170568 p.Ile15Met missense_variant 0.76 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 2289220 c.16_21delATCGTC conservative_inframe_deletion 0.76 pyrazinamide Uncertain significance
eis 2715300 c.33C>T synonymous_variant 0.73 kanamycin Not assoc w R - Interim
amikacin
Rv2681 2996979 p.Gly81Ser missense_variant 0.76 capreomycin Uncertain significance
Rv2752c 3065002 p.His397Leu missense_variant 0.1 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3065527 p.Leu222Arg missense_variant 0.73 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065712 c.480C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.27 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
lpqB 3623990 c.921G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline 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 0.24 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.75 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.71 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243246 p.Gly5Val missense_variant 0.13 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.25 ethambutol Not assoc w R
embB 4246541 p.Ser10Arg missense_variant 0.79 ethambutol
embB 4249582 c.3069G>A synonymous_variant 0.78 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.23 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 0.28 streptomycin Not assoc w R
gid 4407693 p.Glu170Asp missense_variant 0.1 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.27 streptomycin Not assoc w R