TB-Profiler result

Run: ERR4553683
Summary

Run ID: ERR4553683

Sample name:

Date: 2024-10-05T05:54:31.562019

Number of reads: 3106099

Percentage reads mapped: 99.58

Median coverage: 134.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.06
lineage4.1.1.1 Euro-American (X-type) RD183 0.94
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.25
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
rpoC p.Gly332Arg Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Gly105Asp Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
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
gyrB 6738 p.Thr500Asn missense_variant 0.1 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
rpsL 781822 p.Lys88Arg missense_variant 0.99 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288928 p.Gly105Asp missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 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 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
hadA 732110 p.Cys61Gly missense_variant 0.99 isoniazid Uncertain significance
nusG 733898 c.-356C>G upstream_gene_variant 0.94 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854070 c.465C>T synonymous_variant 1.0 linezolid 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 2155617 c.495T>C synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2156129 c.-18A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3074220 c.252A>T synonymous_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640349 c.-193_-190delCCGG upstream_gene_variant 0.12 pretomanid
delamanid
clofazimine
fbiA 3641447 p.Thr302Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
rpoA 3877553 p.Glu319Lys missense_variant 1.0 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327303 c.171C>T synonymous_variant 0.99 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 0.2 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338599 c.-78A>C upstream_gene_variant 0.2 kanamycin
capreomycin
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin