TB-Profiler result

Run: SRR6930935
Summary

Run ID: SRR6930935

Sample name:

Date: 2024-10-05T03:50:36.243345

Number of reads: 3610141

Percentage reads mapped: 99.65

Median coverage: 79.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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.Ser450Leu Assoc w R
isoniazid katG p.Val1Ala Mutation from literature
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Thr142Met Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Asn499Lys Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Asn499Lys 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 6736 p.Asn499Lys missense_variant 1.0 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2156110 p.Val1Ala missense_variant 1.0 isoniazid Mutation from literature
pncA 2288817 p.Thr142Met missense_variant 0.99 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol Uncertain significance Mutation from literature
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 0.99 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759939 p.Pro45Ala missense_variant 1.0 rifampicin Uncertain significance
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154890 p.Phe408Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2156531 c.-435_-421delTGCGCGTGACCCGAC upstream_gene_variant 1.0 isoniazid
PPE35 2168446 p.Pro723Ser missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288839 p.Thr135Ala missense_variant 0.99 pyrazinamide Uncertain significance
ahpC 2726110 c.-83_-82insTC upstream_gene_variant 1.0 isoniazid
Rv2752c 3065855 c.336delT frameshift_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.99 cycloserine
clpC1 4039337 c.1368A>C synonymous_variant 0.98 pyrazinamide
glpK 4138341 c.1414delG frameshift_variant 0.52 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.24 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T 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 4338648 c.-127A>G upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin