TB-Profiler result

Run: SRR10040372
Summary

Run ID: SRR10040372

Sample name:

Date: 2024-10-04T02:13:25.224143

Number of reads: 7214351

Percentage reads mapped: 99.33

Median coverage: 153.0

Strain: lineage4.4.2

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 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
lineage4.4.2 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser493Leu Uncertain significance Mutation from literature
isoniazid katG p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.-427_166del Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.His70Arg Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
gyrA p.His70Arg Uncertain significance Mutation from literature
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide ethA c.103_107dupCTGGA Assoc w R
clofazimine
para-aminosalicylic_acid folC p.Ile43Ser Mutation from literature
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 6742 p.Glu501Asp missense_variant 1.0 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7510 p.His70Arg missense_variant 1.0 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin Assoc w R
rpoB 761284 p.Ser493Leu missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.99 streptomycin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289075 c.-427_166del frameshift_variant&start_lost 1.0 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
folC 2747471 p.Ile43Ser missense_variant 0.99 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4327366 c.103_107dupCTGGA frameshift_variant 1.0 ethionamide 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 1422 p.Met474Ile missense_variant 0.99 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575806 c.460dupC frameshift_variant 0.99 isoniazid Uncertain significance
ethionamide Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 778976 c.-71C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801273 c.465C>G synonymous_variant 0.99 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726757 c.567dupA frameshift_variant 1.0 isoniazid Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
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
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 1.0 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 0.99 kanamycin
capreomycin
amikacin