TB-Profiler result

Run: SRR28646082
Summary

Run ID: SRR28646082

Sample name:

Date: 2024-10-04T06:29:32.178996

Number of reads: 3200554

Percentage reads mapped: 99.25

Median coverage: 84.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.49
lineage4.1.2 Euro-American None 0.5
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.54
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.49
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala146Val Assoc w R
streptomycin gid p.Gln125* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1391dupA Assoc w R
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 0.56 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.58 rifampicin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 0.41 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
pncA 2288805 p.Ala146Val missense_variant 0.48 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.54 ethambutol Assoc w R
ethA 4326082 c.1391dupA frameshift_variant 0.47 ethionamide Assoc w R
gid 4407830 p.Gln125* stop_gained 0.57 streptomycin 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 371 p.Pro124Leu missense_variant 0.6 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13543 p.Trp6Arg missense_variant 0.44 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.44 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.56 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.39 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.44 rifampicin Not assoc w R
rpoC 765008 p.Leu547Val missense_variant 0.48 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.58 rifampicin Not assoc w R
rpoC 766085 p.Pro906Ala missense_variant 0.52 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 777820 c.661C>T synonymous_variant 0.54 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1460992 c.-53A>C upstream_gene_variant 0.48 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.5 linezolid Not assoc w R
tlyA 1917588 c.-352C>T upstream_gene_variant 0.54 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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 2518076 c.-39C>T upstream_gene_variant 0.56 isoniazid
eis 2715432 c.-100C>T upstream_gene_variant 0.54 kanamycin
amikacin
Rv2680 2996136 p.Ser11Asn missense_variant 0.19 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.49 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.4 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.43 cycloserine
rpoA 3878432 c.76C>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.5 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.45 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 0.52 kanamycin
capreomycin
amikacin