TB-Profiler result

Run: ERR161123
Summary

Run ID: ERR161123

Sample name:

Date: 2024-04-15T18:20:14.544406

Number of reads: 4179442

Percentage reads mapped: 99.36

Median coverage: 92.0

Strain: lineage1.2.2.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.1 Indo-Oceanic RD239 0.81
lineage4.3 Euro-American (LAM) None 0.19
lineage1.2.2 Indo-Oceanic RD239 0.85
lineage4 Euro-American None 0.18
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.19
lineage1 Indo-Oceanic RD239 0.82
lineage4.3.4 Euro-American (LAM) RD174 0.18
lineage4.3.4.2 Euro-American (LAM) RD174 0.17
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 237 c.237G>A synonymous_variant 0.89 isoniazid Not assoc w R - Interim
gyrB 5075 c.-165C>T upstream_gene_variant 0.84 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.28 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 8452 p.Ala384Val missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.86 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 13245 p.Glu105Ala missense_variant 0.77 isoniazid Uncertain significance
Rv0010c 13298 p.Ile87Met missense_variant 0.79 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.81 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.81 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620659 p.Arg257Cys missense_variant 0.79 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.84 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.79 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.79 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.19 rifampicin Not assoc w R
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 0.82 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776311 p.Gly724Ser missense_variant 0.13 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.85 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.89 linezolid Uncertain significance
Rv1129c 1254243 p.Glu98Lys missense_variant 0.85 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.85 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.81 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.8 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.83 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474517 n.860C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.79 linezolid Not assoc w R
tsnR 1854247 c.642A>G synonymous_variant 0.69 linezolid
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 0.75 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.98 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.82 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.77 isoniazid
Rv2752c 3064761 c.1431C>T synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3064852 p.Met447Thr missense_variant 0.77 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.22 para-aminosalicylic_acid
thyA 3074553 c.-82C>T upstream_gene_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.78 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.17 pyrazinamide Not assoc w R
Rv3236c 3612865 p.Ser84Arg missense_variant 0.12 pyrazinamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.2 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.2 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.8 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
embC 4240671 p.Thr270Ile missense_variant 0.82 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.81 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.78 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245321 p.Met697Val missense_variant 0.79 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.8 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.78 ethambutol Not assoc w R
aftB 4267517 c.1320A>G synonymous_variant 0.76 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.79 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.89 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.82 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.8 ethionamide Not assoc w R - Interim
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 4338603 c.-82C>T upstream_gene_variant 0.85 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 0.9 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.71 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.22 streptomycin Not assoc w R