TB-Profiler result

Run: 1488fdff-f666-4247-a490-54d09b79d364
Summary

Run ID: 1488fdff-f666-4247-a490-54d09b79d364

Sample name:

Date: 05-08-2023 01:23:56

Number of reads: 353129

Percentage reads mapped: 98.2

Median coverage: 11

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 1.0
lineage1.1 Indo-Oceanic RD239 1.0
lineage1.1.2 Indo-Oceanic RD239 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
gyrB 6124 c.885C>T synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776233 p.Pro750Ser missense_variant 0.12 clofazimine
bedaquiline
mmpL5 776395 p.Phe696Leu missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
embR 1416776 p.Ile191Thr missense_variant 0.17 ethambutol
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2156541 c.-430G>A upstream_gene_variant 0.17 isoniazid
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ribD 2986844 c.6C>T synonymous_variant 0.15 para-aminosalicylic_acid
ribD 2987123 c.285C>T synonymous_variant 0.1 para-aminosalicylic_acid
thyX 3067315 c.631C>T synonymous_variant 0.17 para-aminosalicylic_acid
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474597 c.591C>A synonymous_variant 1.0 capreomycin
amikacin
Rv3236c 3612680 p.Arg146Gln missense_variant 0.2 pyrazinamide
clpC1 4039513 p.Lys398Glu missense_variant 0.15 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Uncertain significance
embA 4245218 c.1986C>T synonymous_variant 1.0 ethambutol
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4249702 c.3189C>T synonymous_variant 0.15 ethambutol
aftB 4267352 c.1485C>T synonymous_variant 0.14 capreomycin
amikacin
ubiA 4269031 p.Gly268Asp missense_variant 1.0 ethambutol Uncertain significance
aftB 4269606 c.-770T>C upstream_gene_variant 1.0 capreomycin
amikacin
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin
gid 4408100 p.Leu35Met missense_variant 0.11 streptomycin Uncertain significance