TB-Profiler result

Run: 44ebb9ff-87fe-49c1-9c13-44be8ad13f92
Summary

Run ID: 44ebb9ff-87fe-49c1-9c13-44be8ad13f92

Sample name:

Date: 13-12-2023 13:34:18

Number of reads: 552848

Percentage reads mapped: 99.08

Median coverage: 17

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.3.3 Euro-American (LAM) RD115 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
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 7234 c.-68C>G upstream_gene_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 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 8040 p.Gly247Ser 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 491027 p.Asn82Thr missense_variant 0.22 delamanid
ccsA 620532 c.642T>G synonymous_variant 0.46 capreomycin
amikacin
rpoB 759615 c.-192A>C upstream_gene_variant 0.2 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.21 rifampicin
rpoB 759939 p.Pro45Ala missense_variant 1.0 rifampicin Uncertain significance
rpoB 760636 p.Pro277Leu missense_variant 0.13 rifampicin
rpoB 761224 c.1419_1420delCT frameshift_variant 0.11 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 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
rpsL 781547 c.-13A>T upstream_gene_variant 0.11 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
katG 2155233 c.879G>A synonymous_variant 0.11 isoniazid
PPE35 2170330 p.Ala95Thr missense_variant 0.13 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2288830 p.Cys138Gly missense_variant 1.0 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 1.0 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
rpoA 3878174 p.Pro112Ser missense_variant 0.13 rifampicin
rpoA 3878177 p.Val111Met missense_variant 0.13 rifampicin
rpoA 3878178 p.Ile110Thr missense_variant 0.13 rifampicin
rpoA 3878182 p.Asp109Gly missense_variant 0.13 rifampicin
ddn 3986919 p.Thr26Pro missense_variant 0.24 delamanid
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide
clpC1 4039484 c.1221T>G synonymous_variant 0.25 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4245843 p.Val871Leu missense_variant 0.17 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.12 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.12 ethambutol Uncertain significance
aftB 4267290 p.Ala516Val missense_variant 0.11 capreomycin Uncertain significance
amikacin Uncertain significance
ethR 4326610 c.-939G>T upstream_gene_variant 1.0 ethionamide
whiB6 4338593 c.-73delT upstream_gene_variant 1.0 streptomycin
capreomycin
amikacin
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0 streptomycin
capreomycin
amikacin
gid 4407952 c.235_250delTTGGCGATAGCGCGGC frameshift_variant 1.0 streptomycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Uncertain significance