TB-Profiler result

Run: SRR6785220
Summary

Run ID: SRR6785220

Sample name:

Date: 2024-04-15T03:26:41.447927

Number of reads: 3903214

Percentage reads mapped: 99.85

Median coverage: 52.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.76
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.21
lineage4.3.3 Euro-American (LAM) RD115 0.81
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.7 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid Assoc w R High-level resistance
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 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8178 p.Asp293Tyr missense_variant 0.78 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.23 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.77 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4 ethionamide
isoniazid
rpsA 1834836 p.Met432Thr missense_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.76 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.78 isoniazid Not assoc w R
PPE35 2168527 p.Gly696* stop_gained 0.27 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.14 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.14 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.88 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.77 para-aminosalicylic_acid
pepQ 2860320 c.99A>G synonymous_variant 0.77 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.14 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.71 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.78 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.65 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626177 p.Pro146Leu missense_variant 0.75 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3840631 p.Pro264Ser missense_variant 0.92 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.82 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247395 c.882C>T synonymous_variant 0.24 ethambutol Not assoc w R - Interim
ethA 4327160 p.Ile105Thr missense_variant 0.22 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.8 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.76 streptomycin Not assoc w R