TB-Profiler result

Run: 05cab069-d8ba-498d-aede-c5e8f86026af
Summary

Run ID: 05cab069-d8ba-498d-aede-c5e8f86026af

Sample name:

Date: 29-03-2024 08:51:25

Number of reads: 5183626

Percentage reads mapped: 98.59

Median coverage: 119

Strain: lineage4.3.4.2.1

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 0.98
lineage4.3.4 Euro-American (LAM) RD174 0.98
lineage4.3.4.2 Euro-American (LAM) RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.97
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
gyrB 5353 c.114T>G synonymous_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6140 p.Val301Leu missense_variant 0.98 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
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
fgd1 490751 c.-32T>G upstream_gene_variant 0.15 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.21 delamanid
mshA 575926 c.579A>C synonymous_variant 0.13 ethionamide
isoniazid
ccsA 620748 c.858T>G synonymous_variant 0.12 capreomycin
amikacin
ccsA 620756 p.Asp289Gly missense_variant 0.13 capreomycin
amikacin
rpoB 759615 c.-192A>C upstream_gene_variant 0.17 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.2 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.98 rifampicin
rpoC 766550 p.Phe1061Val missense_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1303016 p.Val29Gly missense_variant 0.28 delamanid
fbiC 1304159 p.Val410Gly missense_variant 0.11 delamanid
fbiC 1304166 c.1236A>G synonymous_variant 0.12 delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.12 linezolid
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16 linezolid
rrl 1476426 n.2769A>G non_coding_transcript_exon_variant 0.11 linezolid
rrl 1476441 n.2784T>G non_coding_transcript_exon_variant 0.12 linezolid
fabG1 1674076 p.Thr213Pro missense_variant 0.16 ethionamide
isoniazid
inhA 1674952 p.Pro251Ala missense_variant 0.15 ethionamide
isoniazid
inhA 1674966 c.765T>G synonymous_variant 0.19 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2153933 p.Ala727Ser missense_variant 0.12 isoniazid
katG 2155856 p.Thr86Pro missense_variant 0.14 isoniazid
PPE35 2169317 c.1296C>T synonymous_variant 0.19 pyrazinamide
PPE35 2169320 p.Leu431Phe missense_variant 0.17 pyrazinamide
PPE35 2169862 p.Asn251His missense_variant 0.13 pyrazinamide
PPE35 2169866 c.747G>C synonymous_variant 0.17 pyrazinamide
PPE35 2170045 p.Thr190Pro missense_variant 0.14 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ahpC 2726338 p.Val49Gly missense_variant 0.17 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.2 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.12 isoniazid
pepQ 2859904 p.Val172Gly missense_variant 0.17 clofazimine
bedaquiline
Rv2752c 3064745 p.Thr483Pro missense_variant 0.2 rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339273 c.156T>G synonymous_variant 0.13 delamanid
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3612835 c.282T>G synonymous_variant 0.12 pyrazinamide
fbiB 3642734 c.1200G>C synonymous_variant 0.12 delamanid
fbiB 3642744 p.Ala404Ser missense_variant 0.22 delamanid
alr 3840719 c.702A>G synonymous_variant 0.97 cycloserine
rpoA 3878626 c.-119A>C upstream_gene_variant 0.12 rifampicin
ddn 3986994 p.Thr51Pro missense_variant 0.12 delamanid
ddn 3986997 p.Thr52Pro missense_variant 0.23 delamanid
clpC1 4038287 c.2418C>T synonymous_variant 0.98 pyrazinamide
clpC1 4038857 c.1848C>A synonymous_variant 0.18 pyrazinamide
clpC1 4039484 c.1221T>G synonymous_variant 0.13 pyrazinamide
embC 4239793 c.-70A>C upstream_gene_variant 0.11 ethambutol
embC 4239834 c.-29G>C upstream_gene_variant 0.12 ethambutol
embC 4239838 c.-25T>C upstream_gene_variant 0.14 ethambutol
embC 4239842 c.-21C>A upstream_gene_variant 0.19 ethambutol
embC 4239973 c.111T>G synonymous_variant 0.15 ethambutol
embC 4242393 p.Asp844Ala missense_variant 0.12 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242822 p.Val987Gly missense_variant 0.16 ethambutol
embB 4249323 p.Ala937Glu missense_variant 0.15 ethambutol
ubiA 4269502 p.Val111Gly missense_variant 0.11 ethambutol Uncertain significance
aftB 4269504 c.-668A>G upstream_gene_variant 0.11 capreomycin
amikacin
ubiA 4269511 p.Val108Gly missense_variant 0.12 ethambutol
ubiA 4269514 p.Val107Gly missense_variant 0.15 ethambutol
ubiA 4269529 p.Ala102Gly missense_variant 0.14 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.99 streptomycin Uncertain significance