TB-Profiler result

Run: SRR13838016

Summary

Run ID: SRR13838016

Sample name:

Date: 2024-10-04T05:49:48.559015

Number of reads: 2980782

Percentage reads mapped: 96.38

Median coverage: 103.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive


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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
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 1427 p.Ala476Gly missense_variant 0.99 isoniazid
gyrA 7346 p.Ile15Met missense_variant 0.99 levofloxacin
moxifloxacin
gyrA 8335 p.Met345Arg missense_variant 0.98 levofloxacin
moxifloxacin
gyrA 9639 p.Gly780Arg missense_variant 0.97 levofloxacin
moxifloxacin
fgd1 491505 c.723G>A synonymous_variant 1.0 pretomanid
delamanid
clofazimine
mshA 576310 p.Ile321Met missense_variant 1.0 isoniazid
ethionamide
Rv0565c 657451 p.Ala7Val missense_variant 1.0 ethionamide
rpoC 766765 c.3396A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.12 rifampicin
mmpL5 775981 p.Leu834Val missense_variant 1.0 bedaquiline
clofazimine
mmpL5 776732 c.1749C>T synonymous_variant 1.0 bedaquiline
clofazimine
mmpL5 777942 p.Pro180Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800343 c.-466G>C upstream_gene_variant 1.0 linezolid
fbiC 1303422 c.492A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1406592 p.Tyr250Cys missense_variant 1.0 streptomycin
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416737 p.Arg204Gln missense_variant 1.0 ethambutol
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rpsA 1833940 c.399C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834091 p.Val184Met missense_variant 0.96 pyrazinamide
tlyA 1918473 c.534T>A synonymous_variant 0.99 capreomycin
Rv1979c 2221849 p.Leu439Gln missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222231 p.Met312Leu missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222710 p.Asn152Ile missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223809 c.-646_-645insT upstream_gene_variant 1.0 bedaquiline
clofazimine
eis 2714723 p.Cys204Gly missense_variant 1.0 kanamycin
amikacin
folC 2746975 p.Asp208Glu missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782420 c.1623T>A synonymous_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784310 c.-268T>A upstream_gene_variant 0.99 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2860233 c.186T>G synonymous_variant 1.0 bedaquiline
clofazimine
thyA 3073781 p.Leu231Ile missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448420 c.-84_-83insT upstream_gene_variant 1.0 ethionamide
whiB7 3568689 c.-11delT upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
embC 4240494 p.Gly211Ala missense_variant 1.0 ethambutol Uncertain significance
embC 4241732 p.Ala624Pro missense_variant 1.0 ethambutol
embA 4245672 p.Gly814Arg missense_variant 0.98 ethambutol
embB 4247458 p.Tyr315* stop_gained 0.96 ethambutol
aftB 4268265 p.Leu191Gln missense_variant 1.0 ethambutol