TB-Profiler result

Run: SRR19428561
Summary

Run ID: SRR19428561

Sample name:

Date: 2024-10-05T02:21:58.142046

Number of reads: 729669

Percentage reads mapped: 99.45

Median coverage: 34.0

Strain: lineage3;lineage4.2.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.52
lineage3 East-African-Indian RD750 0.45
lineage4.2 Euro-American None 0.55
lineage4 Euro-American None 0.49
lineage4.2.2.2 Euro-American (Ural) None 0.57
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
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 180 c.180T>C synonymous_variant 0.56 isoniazid Not assoc w R - Interim
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 8688 p.Ala463Ser missense_variant 0.4 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
fgd1 491742 c.960T>C synonymous_variant 0.5 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.6 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.6 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.47 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.54 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 767094 p.Ser1242Asn missense_variant 0.65 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.32 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
rplC 800204 c.-605T>C upstream_gene_variant 0.46 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254732 c.-198C>T upstream_gene_variant 0.36 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472866 n.1021C>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
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
bacA 2063685 c.1044G>A synonymous_variant 0.59 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.68 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.5 isoniazid 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
pncA 2289047 c.195C>T synonymous_variant 0.48 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.48 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.58 isoniazid Not assoc w R
folC 2747687 c.-89C>T upstream_gene_variant 0.39 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.54 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3066131 p.Leu21Val missense_variant 0.68 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.41 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.62 cycloserine
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
panD 4044872 c.-591C>T upstream_gene_variant 0.48 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.57 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247611 c.1098G>T synonymous_variant 0.4 ethambutol Not assoc w R - Interim
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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.4 streptomycin Not assoc w R