TB-Profiler result

Run: ERR12544380
Summary

Run ID: ERR12544380

Sample name:

Date: 2024-04-15T23:24:59.901368

Number of reads: 3446001

Percentage reads mapped: 99.66

Median coverage: 124.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.28
lineage4.1 Euro-American None 0.64
lineage4.1.2 Euro-American None 0.66
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.67
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.32
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
lineage4 Euro-American None 0.68
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.36 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid Assoc w R High-level resistance
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 936 c.936C>A synonymous_variant 0.54 isoniazid Not assoc w R - Interim
gyrB 5713 c.474C>G synonymous_variant 0.47 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.73 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.45 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.67 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.18 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.4 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.59 ethionamide Uncertain significance
Rv0565c 657370 p.Gln34Arg missense_variant 0.37 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.65 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.66 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.32 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 0.38 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.37 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.32 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474438 n.781A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 0.41 isoniazid Not assoc w R
PPE35 2167792 p.Ser941Ala missense_variant 0.66 pyrazinamide Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.38 pyrazinamide 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 2518076 c.-39C>T upstream_gene_variant 0.75 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.13 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612660 p.Ser153Ala missense_variant 0.36 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.3 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.38 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878567 c.-60C>G upstream_gene_variant 0.28 rifampicin
rpoA 3878599 c.-92C>G upstream_gene_variant 0.13 rifampicin
rpoA 3878627 c.-120T>G upstream_gene_variant 0.12 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.24 rifampicin Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.64 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 0.62 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.3 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.17 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.21 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.19 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.19 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.18 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.15 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.98 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.43 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.45 streptomycin Not assoc w R
gid 4408436 c.-234C>T upstream_gene_variant 0.65 streptomycin