TB-Profiler result

Run: SRR9613549
Summary

Run ID: SRR9613549

Sample name:

Date: 2024-04-16T04:02:11.442901

Number of reads: 2673947

Percentage reads mapped: 99.89

Median coverage: 43.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.1.1 Euro-American (X-type) RD183 0.87
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.99
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
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 576746 p.Gly467Cys missense_variant 1.0 ethionamide
isoniazid
Rv0565c 657269 p.Ser68Pro missense_variant 0.98 ethionamide Uncertain significance
Rv0565c 657303 c.168C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoB 760493 c.687C>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.96 rifampicin Not assoc w R
rpoC 766070 c.2701C>T synonymous_variant 0.98 rifampicin Not assoc w R
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 800219 c.-590T>C upstream_gene_variant 0.97 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518348 c.234A>T synonymous_variant 0.16 isoniazid
pepQ 2859896 p.Glu175Lys missense_variant 0.97 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.95 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 1.0 rifampicin Not assoc w R
rpoA 3878601 c.-95delG upstream_gene_variant 0.55 rifampicin Uncertain significance
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol Not assoc w R
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