TB-Profiler result

Run: SRR7592356
Summary

Run ID: SRR7592356

Sample name:

Date: 2024-04-14T09:03:09.366439

Number of reads: 2890497

Percentage reads mapped: 99.57

Median coverage: 68.0

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) None 1.0
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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid c.575delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.269dupG Assoc w R
c.613dupG Assoc w R
c.731_732dupGC Assoc w R
kanamycin eis c.-15C>G Uncertain significance Mutation from literature
cycloserine
ethionamide ethA c.56_57dupCG 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
tlyA 1918205 c.269dupG frameshift_variant 0.32 capreomycin Assoc w R
tlyA 1918551 c.613dupG frameshift_variant 0.14 capreomycin Assoc w R
tlyA 1918667 c.731_732dupGC frameshift_variant 0.39 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715347 c.-15C>G upstream_gene_variant 1.0 kanamycin Uncertain significance Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4327416 c.56_57dupCG frameshift_variant 0.91 ethionamide Assoc w R
gid 4407627 c.575delG 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575811 p.Tyr155Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656101 c.1369dupC frameshift_variant 0.71 ethionamide Uncertain significance
Rv0565c 656731 p.Ala247Glu missense_variant 0.34 ethionamide
nusG 733867 c.-386_-381delGCGGTC upstream_gene_variant 1.0 rifampicin
rpoC 765084 p.Arg572His 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289248 c.-7T>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv2681 2997436 p.Arg233Pro missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065479 p.Phe238Ser missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
mtrA 3627595 c.-246G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4039889 c.816G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
ethR 4327826 p.Asn93Ser missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R