TB-Profiler result

Run: SRR1049964
Summary

Run ID: SRR1049964

Sample name:

Date: 2024-10-04T22:05:15.633761

Number of reads: 3272460

Percentage reads mapped: 98.66

Median coverage: 67.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.92
lineage4.1 Euro-American None 0.93
lineage4 Euro-American None 0.97
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 gid c.351delG Assoc w R
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
gid 4407851 c.351delG frameshift_variant 0.89 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
gyrB 5914 p.Asp225Glu missense_variant 0.91 levofloxacin Uncertain significance
moxifloxacin 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
fgd1 491742 c.960T>C synonymous_variant 0.1 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.91 ethionamide Uncertain significance
rpoB 759916 p.Lys37Thr missense_variant 0.95 rifampicin
rpoC 764176 c.807C>T synonymous_variant 0.19 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.96 rifampicin Not assoc w R
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
rpsL 781421 c.-139C>A upstream_gene_variant 0.85 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.93 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
ndh 2103173 c.-132delG upstream_gene_variant 0.14 isoniazid
delamanid
ethionamide
katG 2154369 c.1743G>A synonymous_variant 0.13 isoniazid
katG 2156025 c.87C>A synonymous_variant 0.12 isoniazid Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 0.13 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11 bedaquiline Not assoc w R - Interim
clofazimine 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
ribD 2987615 c.777A>G stop_lost&splice_region_variant 0.19 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624660 p.Ala84Gly missense_variant 0.91 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.9 ethambutol Not assoc w R
embA 4243969 p.Val246Ala missense_variant 0.84 ethambutol
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 4407893 p.Met104Val missense_variant 0.12 streptomycin