TB-Profiler result

Run: SRR13837730
Summary

Run ID: SRR13837730

Sample name:

Date: 2024-04-15T19:49:42.825569

Number of reads: 2938588

Percentage reads mapped: 95.01

Median coverage: 98.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) 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
isoniazid
ethambutol embR p.Ser188Arg Mutation from literature
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
embR 1416784 p.Ser188Arg missense_variant 1.0 ethambutol 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
fgd1 490771 c.-12T>G upstream_gene_variant 0.99 clofazimine
pretomanid
delamanid
mshA 575112 c.-236G>T upstream_gene_variant 1.0 ethionamide
isoniazid
rpoB 761125 c.1320dupG frameshift_variant 0.99 rifampicin
rpoB 761989 p.Ala728Val missense_variant 1.0 rifampicin
rpoC 763884 p.Ala172Asp missense_variant 1.0 rifampicin
rpoC 764514 p.Phe382Tyr missense_variant 1.0 rifampicin
rpoC 765936 p.Ala856Gly missense_variant 1.0 rifampicin
mmpL5 776303 c.2178G>C synonymous_variant 0.99 clofazimine
bedaquiline
rplC 800132 c.-677C>G upstream_gene_variant 1.0 linezolid
fbiC 1303334 p.Gly135Val missense_variant 1.0 clofazimine
pretomanid
delamanid
embR 1416250 c.1098C>A synonymous_variant 1.0 ethambutol
rrl 1474218 n.561T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475718 n.2061T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
fabG1 1673184 c.-256T>C upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1833707 p.Gly56Arg missense_variant 1.0 pyrazinamide
tlyA 1918168 p.Phe77Leu missense_variant 1.0 capreomycin
bacA 2063041 p.Arg563Pro missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063427 c.1302G>T synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063999 c.729_730insT frameshift_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
ndh 2103307 c.-265A>G upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
kasA 2518023 c.-92C>T upstream_gene_variant 1.0 isoniazid
eis 2715279 c.54A>G synonymous_variant 1.0 amikacin
kanamycin
folC 2747689 c.-91C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
fbiD 3339289 p.Ser58Ala missense_variant 1.0 clofazimine
pretomanid
delamanid
whiB7 3569132 c.-453C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
Rv3236c 3613708 c.-592C>G upstream_gene_variant 1.0 pyrazinamide
clpC1 4038389 c.2316G>C synonymous_variant 1.0 pyrazinamide
clpC1 4040326 p.Leu127Val missense_variant 1.0 pyrazinamide
glpK 4139633 c.123C>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4241920 p.Asp686Glu missense_variant 1.0 ethambutol
ubiA 4269209 p.Ser209Thr missense_variant 1.0 ethambutol