TB-Profiler result

Run: ERR037469
Summary

Run ID: ERR037469

Sample name:

Date: 2024-10-04T10:41:14.623509

Number of reads: 21649208

Percentage reads mapped: 99.54

Median coverage: 361.0

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 0.37
lineage4.3 Euro-American (LAM) None 0.65
lineage1.2.2 Indo-Oceanic RD239 0.38
lineage4 Euro-American None 0.65
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.64
lineage1 Indo-Oceanic RD239 0.37
lineage4.3.4 Euro-American (LAM) RD174 0.64
lineage4.3.4.2 Euro-American (LAM) RD174 0.65
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 0.43 isoniazid Not assoc w R - Interim
dnaA 1255 p.Ala419Thr missense_variant 0.62 isoniazid Uncertain significance
gyrB 5075 c.-165C>T upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.59 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 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8489 c.1188A>G synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.37 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 13298 p.Ile87Met missense_variant 0.38 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.29 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.36 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.36 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620659 p.Arg257Cys missense_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.37 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.36 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.38 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.63 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.38 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.36 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.38 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254749 c.-215C>A upstream_gene_variant 0.39 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1417019 p.Cys110Tyr missense_variant 0.34 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.35 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.35 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472555 n.710C>T non_coding_transcript_exon_variant 0.44 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.31 linezolid Not assoc w R
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 0.38 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064885 c.-157G>T upstream_gene_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.42 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.37 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.37 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 0.4 isoniazid
Rv2477c 2784139 c.-98delC upstream_gene_variant 0.37 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.51 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2995801 c.-304C>A upstream_gene_variant 0.38 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.59 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.34 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.67 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.67 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.65 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.34 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.36 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.38 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.35 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.36 ethambutol Not assoc w R
embB 4246870 c.357C>T synonymous_variant 0.34 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.34 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.35 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.41 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.4 ethionamide Not assoc w R - Interim
whiB6 4338371 p.Thr51Pro missense_variant 0.63 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin 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 0.35 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 4407588 c.615A>G synonymous_variant 0.36 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.37 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.64 streptomycin Not assoc w R