TB-Profiler result

Run: 5767ebf3-6e0c-4229-940c-702a974d52d9
Summary

Run ID: 5767ebf3-6e0c-4229-940c-702a974d52d9

Sample name:

Date: 14-05-2024 16:03:43

Number of reads: 11552010

Percentage reads mapped: 97.96

Median coverage: 190

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7493 c.192C>T synonymous_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
rpoB 759620 c.-187A>C upstream_gene_variant 0.24 rifampicin
rpoB 759831 p.Thr9Pro missense_variant 0.28 rifampicin
rpoC 762836 c.-534C>G upstream_gene_variant 0.3 rifampicin
rpoC 764725 p.Phe452Leu missense_variant 0.18 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779371 p.Ala128Pro missense_variant 0.18 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800997 p.Asn63Lys missense_variant 0.24 linezolid
atpE 1460992 c.-53A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
atpE 1461019 c.-26C>A upstream_gene_variant 0.22 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21 linezolid
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18 linezolid
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 1.0 linezolid
fabG1 1673449 p.Thr4Pro missense_variant 0.21 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102891 p.Phe51Ser missense_variant 0.18 ethionamide
isoniazid
PPE35 2167871 c.2742G>C synonymous_variant 0.22 pyrazinamide
PPE35 2169320 p.Leu431Phe missense_variant 0.12 pyrazinamide
PPE35 2169379 p.Phe412Val missense_variant 0.21 pyrazinamide
PPE35 2169866 c.747G>C synonymous_variant 0.28 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2288982 p.Thr87Met missense_variant 0.99 pyrazinamide Uncertain significance
eis 2714366 p.Val323Leu missense_variant 0.21 kanamycin
amikacin
eis 2715586 c.-254G>C upstream_gene_variant 0.42 kanamycin
amikacin
folC 2746186 c.1413G>C synonymous_variant 0.21 para-aminosalicylic_acid
pepQ 2859381 c.1038C>G synonymous_variant 0.18 clofazimine
bedaquiline
ribD 2987307 p.Ala157Pro missense_variant 0.23 para-aminosalicylic_acid
Rv2752c 3064552 p.Arg547Pro missense_variant 0.19 rifampicin
isoniazid
thyX 3067535 c.411C>T synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3073806 c.666C>G synonymous_variant 0.24 para-aminosalicylic_acid
fprA 3474601 p.Arg199Gly missense_variant 0.24 capreomycin
amikacin
fprA 3475280 p.Val425Gly missense_variant 0.22 capreomycin
amikacin
fbiB 3641955 p.Gly141Arg missense_variant 0.25 delamanid
fbiB 3642734 c.1200G>C synonymous_variant 0.26 delamanid
fbiB 3642772 p.Asp413Ala missense_variant 0.17 delamanid
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
rpoA 3878051 p.Arg153Trp missense_variant 1.0 rifampicin Uncertain significance
ddn 3987013 p.Gly57Ala missense_variant 0.19 delamanid
clpC1 4038857 c.1848C>A synonymous_variant 0.19 pyrazinamide
clpC1 4039932 p.Gly258Val missense_variant 0.26 pyrazinamide
embC 4239842 c.-21C>A upstream_gene_variant 0.13 ethambutol
embC 4242425 p.Arg855Gly missense_variant 0.16 ethambutol
embC 4242476 p.Pro872Ala missense_variant 0.28 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242822 p.Val987Gly missense_variant 0.42 ethambutol
embC 4242827 p.Leu989Val missense_variant 0.18 ethambutol
ubiA 4269529 p.Ala102Gly missense_variant 0.19 ethambutol
ethA 4327672 c.-199G>A upstream_gene_variant 0.19 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv3083 3448498 c.-5_*1408del transcript_ablation 1.0 ethionamide