TB-Profiler result

Run: SRR11972257
Summary

Run ID: SRR11972257

Sample name:

Date: 2024-04-15T02:45:20.445151

Number of reads: 321625

Percentage reads mapped: 99.33

Median coverage: 10.0

Strain: lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.95
lineage4 Euro-American None 0.12
lineage1.1.3.1 Indo-Oceanic RD239 0.87
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
gyrB 6112 p.Met291Ile missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.92 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.94 isoniazid Not assoc w R
nusG 734116 c.-138T>C upstream_gene_variant 0.8 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 1.0 rifampicin Not assoc w R
mmpL5 777572 c.909C>T synonymous_variant 0.79 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rplC 800357 c.-452C>A upstream_gene_variant 0.73 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.86 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254615 c.-81G>A upstream_gene_variant 0.64 moxifloxacin
levofloxacin
rifampicin
isoniazid
embR 1417554 c.-207C>G upstream_gene_variant 0.89 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854045 p.Tyr147Cys missense_variant 0.9 linezolid Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.8 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.77 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.73 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.81 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 0.83 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841253 c.168C>T synonymous_variant 0.94 cycloserine
alr 3841277 c.144C>T synonymous_variant 0.95 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.83 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.93 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.68 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.91 ethambutol Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.91 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.91 streptomycin Not assoc w R