TB-Profiler result

Run: SRR19276615
Summary

Run ID: SRR19276615

Sample name:

Date: 2024-04-16T11:00:03.165001

Number of reads: 2140327

Percentage reads mapped: 99.72

Median coverage: 77.0

Strain: lineage4

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 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.His445Asp Assoc w R
p.Leu449Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid inhA p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Leu587Pro Uncertain significance Mutation from literature
ethambutol embB p.Gly406Asp Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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 761139 p.His445Asp missense_variant 1.0 rifampicin Assoc w R
rpoB 761152 p.Leu449Gln missense_variant 0.14 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim
katG 2154352 p.Leu587Pro missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 1.0 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 1456 p.Glu486Lys missense_variant 1.0 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
rpoB 761889 p.Val695Leu missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rplC 801009 c.201A>G synonymous_variant 1.0 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471890 n.45G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156118 c.-7G>T upstream_gene_variant 0.82 isoniazid Uncertain significance
katG 2156205 c.-94T>C upstream_gene_variant 0.39 isoniazid
katG 2156351 c.-338_-241delGCCCGACGTATCCCGGCAAGCCGTGTACGACGTGCTGCATGCCCTGACCGCCGCGGGCTTGGTGCGAAAGATCCAACCCTCGGGCTCCGTCGCGCGCT upstream_gene_variant 0.56 isoniazid Uncertain significance
katG 2156625 c.-514C>T upstream_gene_variant 0.25 isoniazid
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065517 c.675C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0 ethionamide
mtrB 3626352 p.Val88Ile missense_variant 0.35 bedaquiline
rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269722 p.Ala38Thr missense_variant 1.0 ethambutol Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 1.0 ethionamide
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