TB-Profiler result

Run: ERR025437
Summary

Run ID: ERR025437

Sample name:

Date: 2024-10-05T11:04:00.315163

Number of reads: 754225

Percentage reads mapped: 99.27

Median coverage: 16.0

Strain: lineage1.2.1.2.1;lineage2.2.2;lineage4.1.2;lineage4.2.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.06
lineage1.2.1.2 Indo-Oceanic RD239 0.65
lineage2 East-Asian RD105 0.06
lineage4.1.2 Euro-American None 0.1
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.05
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage4 Euro-American None 0.29
lineage1 Indo-Oceanic RD239 0.64
lineage1.2.1.2.1 Indo-Oceanic RD239 0.62
lineage1.2.1 Indo-Oceanic RD239 0.59
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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1343delA Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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
ethA 4326130 c.1343delA frameshift_variant 0.36 ethionamide 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
dnaA 1302 c.1302C>A synonymous_variant 0.48 isoniazid Not assoc w R
gyrB 6112 p.Met291Ile missense_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13175 c.384T>C synonymous_variant 0.67 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.57 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.78 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.58 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.64 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.8 rifampicin Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 778743 p.Val55Met missense_variant 0.36 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.52 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.75 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.62 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.62 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.83 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.58 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.37 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.58 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.59 ethionamide Uncertain significance
whiB7 3568488 c.191delG frameshift_variant 0.68 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.61 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.76 pyrazinamide Not assoc w R - Interim
embC 4241042 p.Asn394Asp missense_variant 0.71 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.62 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.59 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.65 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.69 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.58 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407873 c.330G>T synonymous_variant 0.82 streptomycin Not assoc w R