TB-Profiler result

Run: ERR2706927
Summary

Run ID: ERR2706927

Sample name:

Date: 2024-10-05T12:32:56.969744

Number of reads: 4616315

Percentage reads mapped: 99.58

Median coverage: 138.0

Strain: lineage1.1.3.1;lineage4.7

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.36
lineage1.1 Indo-Oceanic RD239 0.34
lineage4.7 Euro-American (mainly T) None 0.63
lineage4 Euro-American None 0.63
lineage1 Indo-Oceanic RD239 0.36
lineage1.1.3.1 Indo-Oceanic RD239 0.37
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
p.Ile480Val Uncertain significance Mutation from literature
isoniazid
ethambutol embB p.Gly406Asp Assoc w R
pyrazinamide pncA c.387delT Assoc w R
p.Leu4Ser Assoc w R
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 761101 p.Gln432Pro missense_variant 0.65 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.66 rifampicin Uncertain significance Mutation from literature
pncA 2288854 c.387delT frameshift_variant 0.15 pyrazinamide Assoc w R
pncA 2289231 p.Leu4Ser missense_variant 0.53 pyrazinamide Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.64 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 968 p.Glu323Ala missense_variant 0.67 isoniazid Uncertain significance
gyrB 5731 c.492C>T synonymous_variant 0.41 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6798 p.Gly520Ala missense_variant 0.62 levofloxacin Not assoc w R
moxifloxacin 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 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.3 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.39 isoniazid Not assoc w R
Rv0010c 13507 p.Ala18Thr missense_variant 0.36 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.31 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575578 c.231G>C synonymous_variant 0.65 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.34 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.35 rifampicin Not assoc w R
mmaA3 738234 c.-85C>T upstream_gene_variant 0.66 isoniazid
rpoB 761823 p.Asn673His missense_variant 0.68 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.41 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.34 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.33 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.34 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 0.35 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777628 p.Tyr285His missense_variant 0.36 bedaquiline
clofazimine
mmpS5 779526 c.-621G>A upstream_gene_variant 0.36 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.36 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.37 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.3 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.38 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.38 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.3 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.21 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.43 isoniazid Not assoc w R
katG 2155213 p.Trp300Ser missense_variant 0.59 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.31 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.32 pyrazinamide Uncertain significance
PPE35 2169104 p.Leu503Phe missense_variant 0.33 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.43 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 0.42 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26 isoniazid
ribD 2987276 c.438G>C synonymous_variant 0.31 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.36 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.36 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.39 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.4 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841253 c.168C>T synonymous_variant 0.3 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.39 pyrazinamide Not assoc w R - Interim
clpC1 4040770 c.-66C>T upstream_gene_variant 0.41 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.21 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.33 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.36 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.39 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.34 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.3 ethambutol Not assoc w R
embB 4248161 c.1648C>T synonymous_variant 0.36 ethambutol Not assoc w R - Interim
embB 4249732 c.3219C>G synonymous_variant 0.83 ethambutol Not assoc w R
aftB 4267992 p.Thr282Met missense_variant 0.64 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.39 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.34 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
gid 4407588 c.615A>G synonymous_variant 0.34 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.26 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.32 streptomycin Not assoc w R
gid 4407993 p.Ser70Arg missense_variant 0.72 streptomycin Uncertain significance