TB-Profiler result

Run: SRR13837992
Summary

Run ID: SRR13837992

Sample name:

Date: 2024-04-15T14:54:10.879340

Number of reads: 884364

Percentage reads mapped: 95.31

Median coverage: 30.0

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 1425 c.1426dupG frameshift_variant 1.0 isoniazid Uncertain significance
rpoB 760475 c.669A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760728 p.Tyr308Asn missense_variant 1.0 rifampicin
rpoC 763928 p.Glu187* stop_gained 1.0 rifampicin
rpoC 766155 p.Ala929Val missense_variant 1.0 rifampicin
mmpL5 777185 c.1296G>T synonymous_variant 1.0 clofazimine
bedaquiline
fbiC 1302932 p.Val1Gly missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1303151 p.Gly74Asp missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304895 c.1965C>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1305298 p.Lys790Gln missense_variant 0.97 clofazimine
pretomanid
delamanid
Rv1258c 1406311 c.1030C>T synonymous_variant 1.0 streptomycin
isoniazid
pyrazinamide
rpsA 1834275 p.Ile245Thr missense_variant 0.97 pyrazinamide
tlyA 1917936 c.-4C>A upstream_gene_variant 1.0 capreomycin
bacA 2064894 c.-166C>G upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2101676 p.Ala456Val missense_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2170823 c.-212delT upstream_gene_variant 1.0 pyrazinamide
pncA 2289356 c.-115G>T upstream_gene_variant 1.0 pyrazinamide
kasA 2518234 p.Glu40Asp missense_variant 1.0 isoniazid
Rv2752c 3064837 p.Leu452Trp missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv3083 3449643 p.Asn380Lys missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3611967 p.Ser384Pro missense_variant 1.0 pyrazinamide
rpoA 3877756 p.Ile251Thr missense_variant 1.0 rifampicin
rpoA 3878065 p.Pro148Arg missense_variant 0.97 rifampicin
ddn 3986977 p.Pro45Arg missense_variant 1.0 delamanid
pretomanid
clpC1 4040538 p.Leu56Arg missense_variant 1.0 pyrazinamide
glpK 4138636 p.Arg374Gly missense_variant 0.97 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embA 4245342 p.Ser704Pro missense_variant 1.0 ethambutol
embB 4248711 c.2198_2199insT frameshift_variant 1.0 ethambutol
aftB 4267498 p.Glu447Lys missense_variant 1.0 ethambutol Uncertain significance
aftB 4268559 p.Leu93Gln missense_variant 1.0 ethambutol
whiB6 4338743 c.-223_-222insC upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin