TB-Profiler result

Run: SRR29050899
Summary

Run ID: SRR29050899

Sample name:

Date: 2024-10-04T04:53:22.366161

Number of reads: 1455798

Percentage reads mapped: 99.74

Median coverage: 40.0

Strain: lineage4.1.2.1;lineage4.3.4.2

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 0.61
lineage4.1 Euro-American None 0.36
lineage4.1.2 Euro-American None 0.37
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.4
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.6
lineage4.3.4.2 Euro-American (LAM) RD174 0.6
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.Asp419His Uncertain significance Mutation from literature
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
katG 2154857 p.Asp419His missense_variant 0.37 isoniazid Uncertain significance Mutation from literature
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 4966 c.-274C>G upstream_gene_variant 0.47 levofloxacin
moxifloxacin
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 9022 p.Gly574Ala missense_variant 0.56 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.47 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.37 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619684 c.-207G>A upstream_gene_variant 0.67 kanamycin
capreomycin
amikacin
Rv0565c 657269 p.Ser68Pro missense_variant 0.47 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.31 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 775915 p.Ala856Ser missense_variant 0.47 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1407489 c.-149G>A upstream_gene_variant 0.33 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
katG 2155357 p.Phe252Tyr missense_variant 0.16 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.26 isoniazid
Rv2752c 3065621 p.Leu191Phe missense_variant 0.62 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066299 c.-108C>T upstream_gene_variant 0.43 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.55 para-aminosalicylic_acid
ald 3086715 c.-105T>C upstream_gene_variant 0.55 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.54 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.47 rifampicin
bedaquiline
clpC1 4038287 c.2418C>T synonymous_variant 0.54 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.49 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.5 ethambutol 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 0.97 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.6 streptomycin Not assoc w R