TB-Profiler result

Run: ERR4827606
Summary

Run ID: ERR4827606

Sample name:

Date: 2024-04-15T09:25:56.856461

Number of reads: 5985960

Percentage reads mapped: 99.63

Median coverage: 188.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.45
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.44
lineage2.2 East-Asian (Beijing) RD105;RD207 0.43
lineage4 Euro-American None 0.55
lineage4.8 Euro-American (mainly T) RD219 0.58
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid katG p.Tyr28* Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
c.-57C>T Uncertain significance Mutation from literature
c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA c.206_216delCACCGCATTGC Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg 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 761161 p.Leu452Pro missense_variant 0.46 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.54 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.44 streptomycin Assoc w R
katG 2156028 p.Tyr28* stop_gained 0.55 isoniazid Assoc w R High-level resistance
pncA 2289025 c.206_216delCACCGCATTGC frameshift_variant 0.24 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.25 isoniazid Uncertain significance Mutation from literature
ahpC 2726136 c.-57C>T upstream_gene_variant 0.18 isoniazid Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 0.59 isoniazid Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.42 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 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.45 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.38 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.53 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.43 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.42 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.61 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.45 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 0.42 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.46 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253330 p.Gly402Glu missense_variant 0.41 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.46 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 0.46 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.39 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417752 c.-405G>A upstream_gene_variant 0.55 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.42 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 0.46 isoniazid Not assoc w R
katG 2155725 c.384_386delGTT disruptive_inframe_deletion 0.37 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.45 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.56 pyrazinamide Not assoc w R
PPE35 2169221 c.1392T>C synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
PPE35 2170623 c.-11G>A upstream_gene_variant 0.4 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288772 p.Val157Gly missense_variant 0.2 pyrazinamide Uncertain significance
eis 2714955 c.378C>T synonymous_variant 0.47 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
folC 2746448 p.Asp384Ala missense_variant 0.45 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.54 capreomycin
Rv2752c 3064714 p.His493Pro missense_variant 0.19 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3074422 p.Pro17Leu missense_variant 0.59 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.49 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.49 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.51 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.52 pyrazinamide Not assoc w R
glpK 4138812 p.Pro315Leu missense_variant 0.52 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139952 c.-197C>G upstream_gene_variant 0.46 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.47 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.41 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 0.25 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.44 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.49 streptomycin Not assoc w R
gid 4408418 c.-216C>T upstream_gene_variant 0.15 streptomycin