TB-Profiler result

Run: 22509df0-e4c1-43c8-a09b-323b2aa9a6df
Summary

Run ID: 22509df0-e4c1-43c8-a09b-323b2aa9a6df

Sample name:

Date: 13-02-2023 03:34:45

Number of reads: 1188706

Percentage reads mapped: 89.95

Median coverage: 24

Strain: lineage4.5

Spoligotype:

Drug-resistance: Other

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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
lineage4.5 Euro-American RD122 0.98
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 pncA p.Arg140His Uncertain significance
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
pncA 2288823 p.Arg140His missense_variant 0.12 pyrazinamide Uncertain significance
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 5548 c.309A>G 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 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7736 c.435C>A synonymous_variant 0.1 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 7892 c.591G>A 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
ccsA 620029 c.139C>T synonymous_variant 0.93 capreomycin
amikacin
rpoC 764380 c.1011G>C synonymous_variant 0.15 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.17 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777238 p.Tyr415His missense_variant 1.0 clofazimine
bedaquiline
mmpL5 778272 p.Pro70Gln missense_variant 0.11 clofazimine
bedaquiline
mmpS5 779499 c.-594C>T upstream_gene_variant 0.12 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1258c 1406101 p.Pro414Ser missense_variant 0.94 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.18 linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.16 linezolid
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.1 linezolid
rpsA 1834956 p.Ala472Asp missense_variant 0.3 pyrazinamide
tlyA 1917948 c.9A>T synonymous_variant 0.1 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
PPE35 2170048 p.Leu189Val missense_variant 0.18 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.17 pyrazinamide
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv2752c 3064556 p.Arg546Cys missense_variant 0.11 rifampicin
isoniazid
Rv2752c 3064822 p.Val457Ala missense_variant 0.12 rifampicin
isoniazid
Rv2752c 3064825 p.Asp456Val missense_variant 0.14 rifampicin
isoniazid
fbiD 3339608 p.Pro164Leu missense_variant 0.11 delamanid
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95 capreomycin
amikacin
Rv3236c 3612526 c.591G>T synonymous_variant 0.15 pyrazinamide
rpoA 3878575 c.-68C>T upstream_gene_variant 0.92 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.18 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.96 pyrazinamide Uncertain significance
clpC1 4040830 c.-126G>A upstream_gene_variant 0.14 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4244176 p.Ala315Gly missense_variant 0.11 ethambutol
embA 4244686 p.Ile485Thr missense_variant 1.0 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.57 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.55 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.46 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.45 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.48 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.48 ethambutol
embB 4249744 c.3231G>A synonymous_variant 0.12 ethambutol
embB 4249751 c.3238T>C synonymous_variant 0.13 ethambutol
ubiA 4269503 p.Val111Met missense_variant 0.12 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance