TB-Profiler result

Run: ERR8479580
Summary

Run ID: ERR8479580

Sample name:

Date: 2024-10-04T13:11:11.346277

Number of reads: 2607534

Percentage reads mapped: 99.48

Median coverage: 98.0

Strain: lineage1.2.2.1;lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

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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 0.52
lineage1.2.2 Indo-Oceanic RD239 0.52
lineage4.1 Euro-American None 0.47
lineage4.1.1.1 Euro-American (X-type) RD183 0.43
lineage4 Euro-American None 0.46
lineage4.1.1 Euro-American (X-type) None 0.45
lineage1 Indo-Oceanic RD239 0.56
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 rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.380_392dupGCGCCCTCACCTG 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.5 streptomycin Assoc w R
ethA 4327081 c.380_392dupGCGCCCTCACCTG frameshift_variant 0.31 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 237 c.237G>A synonymous_variant 0.46 isoniazid Not assoc w R - Interim
gyrB 5075 c.-165C>T upstream_gene_variant 0.47 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.49 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.51 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 0.59 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.58 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.5 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.5 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574643 c.-705C>G upstream_gene_variant 0.64 isoniazid
ethionamide
ccsA 620659 p.Arg257Cys missense_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.41 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.49 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.61 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.49 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.44 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 0.59 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 800219 c.-590T>C upstream_gene_variant 0.49 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.53 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.55 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.54 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.53 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.52 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853490 c.-116C>G upstream_gene_variant 0.38 linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.65 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.54 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 0.49 isoniazid Not assoc w R
katG 2154807 c.1305C>T synonymous_variant 0.46 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.46 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 0.53 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.55 isoniazid
ahpC 2726210 c.18T>C synonymous_variant 0.52 isoniazid Not assoc w R - Interim
ribD 2986836 c.-3G>A upstream_gene_variant 0.41 para-aminosalicylic_acid
thyX 3068115 c.-170C>T upstream_gene_variant 0.63 para-aminosalicylic_acid
thyA 3074034 c.438T>C synonymous_variant 0.63 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.57 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.59 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 0.46 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
rpoA 3877553 p.Glu319Lys missense_variant 0.46 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.49 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.6 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
embC 4240671 p.Thr270Ile missense_variant 0.54 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.58 ethambutol Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.37 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.6 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.44 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.57 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.57 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.41 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.53 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.6 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.37 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.43 ethionamide Not assoc w R - Interim
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 0.61 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 0.47 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.48 streptomycin Not assoc w R