TB-Profiler result

Run: da5ac4ff-c8bb-4ebc-b407-d63b33a5b63e
Summary

Run ID: da5ac4ff-c8bb-4ebc-b407-d63b33a5b63e

Sample name:

Date: 30-04-2024 08:09:06

Number of reads: 671006

Percentage reads mapped: 98.76

Median coverage: 18

Strain: lineage4.3.2

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.2 Euro-American (LAM) 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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9387 p.Ala696Thr missense_variant 0.18 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
rpoC 763613 p.Val82Leu missense_variant 0.13 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin
rpoC 765324 p.Gly652Asp missense_variant 0.12 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777119 p.His454Gln missense_variant 0.11 clofazimine Uncertain significance
bedaquiline
mmpL5 777122 c.1359C>T synonymous_variant 0.11 clofazimine
bedaquiline
mmpL5 777128 c.1353A>G synonymous_variant 0.11 clofazimine
bedaquiline
mmpL5 777522 p.Ala320Val missense_variant 0.1 clofazimine
bedaquiline
mmpR5 779333 p.Gln115Arg missense_variant 0.13 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1303630 p.Pro234Thr missense_variant 0.11 delamanid
fbiC 1303643 p.Pro238Gln missense_variant 0.11 delamanid
fbiC 1304207 p.Arg426Leu missense_variant 0.14 delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
fabG1 1673560 p.Lys41Leu missense_variant 0.23 ethionamide
isoniazid
tlyA 1917948 c.9A>G synonymous_variant 0.14 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102198 p.Ala282Asp missense_variant 0.12 ethionamide
isoniazid
ndh 2102541 p.Ala168Ser missense_variant 0.12 ethionamide
isoniazid
katG 2156539 c.-428G>T upstream_gene_variant 0.14 isoniazid
PPE35 2167745 p.Thr956Arg missense_variant 0.18 pyrazinamide
PPE35 2167965 p.Ala883Gly missense_variant 0.17 pyrazinamide
PPE35 2167967 c.2646A>C synonymous_variant 0.15 pyrazinamide
PPE35 2169133 p.Ala494Thr missense_variant 0.12 pyrazinamide
PPE35 2169287 c.1326T>C synonymous_variant 0.15 pyrazinamide
PPE35 2169293 c.1320T>C synonymous_variant 0.15 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.38 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.4 pyrazinamide
pncA 2289115 p.His43Tyr missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2519140 c.1026G>C synonymous_variant 0.12 isoniazid
kasA 2519143 c.1029G>C synonymous_variant 0.12 isoniazid
kasA 2519153 p.Ile347Val missense_variant 0.12 isoniazid
eis 2715286 p.Met16Lys missense_variant 0.17 kanamycin
amikacin
ribD 2987451 c.614_616delGTG disruptive_inframe_deletion 0.12 para-aminosalicylic_acid
ribD 2987458 c.620_621insCAC disruptive_inframe_insertion 0.12 para-aminosalicylic_acid
Rv2752c 3065220 c.972C>A synonymous_variant 0.18 rifampicin
isoniazid
Rv2752c 3066170 c.21delG frameshift_variant 0.12 rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474653 p.Ala216Val missense_variant 0.2 capreomycin
amikacin
Rv3236c 3612361 c.756C>T synonymous_variant 1.0 pyrazinamide
Rv3236c 3612398 p.Ala240Val missense_variant 0.2 pyrazinamide
Rv3236c 3612955 c.162C>A synonymous_variant 0.2 pyrazinamide
fbiB 3641376 c.-159G>A upstream_gene_variant 0.11 delamanid
fbiB 3641614 c.83_105delATCTGAGCGCCGCCGTCGCCGCG frameshift_variant 0.14 delamanid
alr 3841296 p.Leu42Pro missense_variant 0.1 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide
clpC1 4039153 p.Ile518Val missense_variant 0.13 pyrazinamide
clpC1 4039161 p.His515Gly missense_variant 0.13 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.13 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.12 pyrazinamide
clpC1 4040745 c.-41G>A upstream_gene_variant 0.17 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.17 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.23 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.25 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.25 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.18 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.18 ethambutol
aftB 4267236 p.Pro534Leu missense_variant 0.12 capreomycin
amikacin
ubiA 4269295 p.Met180Thr missense_variant 0.13 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance