TB-Profiler result

Run: SRR6480494
Summary

Run ID: SRR6480494

Sample name:

Date: 2024-10-04T17:02:35.276398

Number of reads: 1756830

Percentage reads mapped: 99.65

Median coverage: 37.0

Strain: lineage1.2.1.2.1;lineage4.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.13
lineage4.3 Euro-American (LAM) None 0.83
lineage4 Euro-American None 0.91
lineage1 Indo-Oceanic RD239 0.08
lineage1.2.1.2.1 Indo-Oceanic RD239 0.07
lineage1.2.1 Indo-Oceanic RD239 0.1
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
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
rpoB 763031 c.3225T>C synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.89 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776686 p.Ser599Ala missense_variant 0.85 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1305181 c.2251T>C synonymous_variant 0.85 pretomanid
delamanid
clofazimine
embR 1417554 c.-207C>G upstream_gene_variant 0.22 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.23 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674162 c.-40C>T upstream_gene_variant 0.29 isoniazid Not assoc w R
ethionamide Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.17 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.24 isoniazid
thyX 3067493 p.Glu151Asp missense_variant 0.77 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.91 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640557 c.15T>C synonymous_variant 0.3 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244420 c.1188G>C synonymous_variant 0.19 ethambutol Not assoc w R
embB 4247578 c.1065G>A synonymous_variant 0.21 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 0.23 ethambutol Not assoc w R
whiB6 4338361 p.Arg54Gln missense_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.16 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.17 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.79 streptomycin Not assoc w R