TB-Profiler result

Run: ERR031483
Summary

Run ID: ERR031483

Sample name:

Date: 2024-04-15T03:59:13.073678

Number of reads: 853815

Percentage reads mapped: 98.33

Median coverage: 16.0

Strain: lineage2.2.1.2;lineage4.3.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.24
lineage4.3 Euro-American (LAM) None 0.25
lineage2 East-Asian RD105 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.12
lineage2.2 East-Asian (Beijing) RD105;RD207 0.06
lineage6.1.3 West-Africa 2 RD702 0.08
lineage4 Euro-American None 0.45
lineage1.2.1.2.1 Indo-Oceanic RD239 0.38
lineage1.2.1 Indo-Oceanic RD239 0.27
lineage4.3.4 Euro-American (LAM) RD174 0.08
lineage4.3.4.2 Euro-American (LAM) RD174 0.07
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 0.12
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
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
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 0.5 isoniazid Not assoc w R
gyrB 6112 p.Met291Ile missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 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 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13175 c.384T>C synonymous_variant 0.41 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.87 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.64 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.62 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.72 ethambutol
atpE 1460907 c.-138T>C upstream_gene_variant 0.33 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.93 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.45 isoniazid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.45 isoniazid
kasA 2519048 p.Gly312Ser missense_variant 0.5 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.5 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.44 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.71 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 0.73 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.56 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.48 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.57 streptomycin Not assoc w R