TB-Profiler result

Run: ERR1035319
Summary

Run ID: ERR1035319

Sample name:

Date: 2024-04-16T06:46:18.491841

Number of reads: 7098518

Percentage reads mapped: 99.6

Median coverage: 140.0

Strain: lineage4.3.3;lineage4.6.4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.15
lineage4.6 Euro-American None 0.86
lineage4.6.4 Euro-American None 0.86
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.16
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 pncA p.Thr76Pro Assoc w R
streptomycin rpsL p.Lys88Met 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 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Met missense_variant 0.16 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289016 p.Thr76Pro missense_variant 0.97 pyrazinamide 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 29 p.Thr10Ser missense_variant 0.9 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 8040 p.Gly247Ser missense_variant 0.15 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 13569 c.-11C>A upstream_gene_variant 0.89 isoniazid Uncertain significance
rpoB 762715 p.Val970Ala missense_variant 0.82 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254144 p.Thr131Pro missense_variant 0.89 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674685 p.Thr162Ala missense_variant 0.91 ethionamide
isoniazid
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 2156724 c.-613C>T upstream_gene_variant 0.84 isoniazid
Rv1979c 2222795 p.Asp124Asn missense_variant 0.87 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288792 c.450C>T synonymous_variant 0.92 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.15 isoniazid
eis 2714393 p.Val314Leu missense_variant 0.83 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2783928 p.Pro39Ser missense_variant 0.86 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.11 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625390 c.-480C>T upstream_gene_variant 0.89 bedaquiline
rifampicin
fbiA 3641176 p.Ala212Pro missense_variant 0.14 clofazimine
pretomanid
delamanid
rpoA 3878745 c.-238C>G upstream_gene_variant 0.88 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.16 pyrazinamide Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGC frameshift_variant&missense_variant 0.85 ethambutol
embB 4248437 p.Thr642Ala missense_variant 0.1 ethambutol Uncertain significance
aftB 4268040 p.Leu266Pro missense_variant 0.2 ethambutol Uncertain significance
ethA 4326693 p.Arg261Trp missense_variant 0.85 ethionamide Uncertain significance
ethA 4327229 p.Leu82Pro missense_variant 0.1 ethionamide Uncertain significance
whiB6 4338546 c.-25G>C upstream_gene_variant 0.85 capreomycin
amikacin
kanamycin
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 4407946 p.Leu86Pro missense_variant 0.92 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.16 streptomycin Not assoc w R