TB-Profiler result

Run: ERR13267119
Summary

Run ID: ERR13267119

Sample name:

Date: 2024-10-04T01:24:44.876576

Number of reads: 2639496

Percentage reads mapped: 99.62

Median coverage: 74.0

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 0.79
lineage4.1 Euro-American None 0.13
lineage4.1.2 Euro-American None 0.16
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.14
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Thr177Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Ile43Thr Mutation from literature
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
gyrA 7582 p.Asp94Gly missense_variant 0.75 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpsL 781687 p.Lys43Arg missense_variant 0.73 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid Assoc w R High-level resistance
pncA 2288713 p.Thr177Pro missense_variant 0.67 pyrazinamide Assoc w R
folC 2747471 p.Ile43Thr missense_variant 0.75 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.82 ethambutol 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
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.22 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.88 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.16 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.82 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.16 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.81 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.19 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 0.79 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.71 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303326 c.396C>T synonymous_variant 0.7 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
tsnR 1854152 p.Gln183* stop_gained 0.23 linezolid Uncertain significance
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 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
Rv1979c 2222357 p.Thr270Ala missense_variant 0.76 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.12 isoniazid
eis 2715716 c.-385delG upstream_gene_variant 0.17 kanamycin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.86 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.23 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.17 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 0.12 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
embB 4247337 p.Thr275Asn missense_variant 0.14 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.79 ethambutol Not assoc w R
whiB6 4338238 p.Leu95Arg missense_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.92 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R