TB-Profiler result

Run: ERR10748114
Summary

Run ID: ERR10748114

Sample name:

Date: 2024-04-15T06:22:23.443169

Number of reads: 1537807

Percentage reads mapped: 99.92

Median coverage: 80.0

Strain: lineage2.2.1;lineage4.8.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.3
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.27
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage4 Euro-American None 0.72
lineage4.8 Euro-American (mainly T) RD219 0.72
lineage4.8.1 Euro-American (mainly T) RD219 0.73
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Thr160Ala Not assoc w R - Interim Mutation from literature
p.Thr100Ile Uncertain significance Mutation from literature
streptomycin
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 ethA p.Gly43Cys Uncertain significance Mutation from literature
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
gyrA 7582 p.Asp94Gly missense_variant 0.41 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Ala missense_variant 0.42 pyrazinamide Not assoc w R - Interim Mutation from literature
pncA 2288943 p.Thr100Ile missense_variant 0.4 pyrazinamide Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.28 ethambutol Assoc w R
ethA 4327347 p.Gly43Cys missense_variant 0.34 ethionamide Uncertain significance Mutation from literature
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 7114 c.-188C>G upstream_gene_variant 0.67 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491328 c.546C>G synonymous_variant 0.37 clofazimine
pretomanid
delamanid
fgd1 491330 p.Lys183Met missense_variant 0.36 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.3 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.28 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.39 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.45 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.23 rifampicin Not assoc w R
rpoC 764822 p.Asp485Tyr missense_variant 0.23 rifampicin Uncertain significance
mmpL5 775592 c.2889G>A synonymous_variant 0.21 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
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 0.28 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.3 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24 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 0.19 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.64 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1833288 c.-254T>C upstream_gene_variant 0.75 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.17 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 0.31 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.26 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.68 pyrazinamide Not assoc w R
PPE35 2170892 c.-280G>A upstream_gene_variant 0.65 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.72 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.32 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 0.59 clofazimine
pretomanid
delamanid
Rv3083 3449315 p.Trp271* stop_gained 1.0 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.34 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.18 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642874 p.Leu447Arg missense_variant 0.74 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.25 ethambutol Not assoc w R
embB 4247717 p.Leu402Val missense_variant 0.37 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.14 ethambutol Not assoc w R
whiB6 4338365 p.Cys53Arg missense_variant 0.21 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 0.21 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.31 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.37 streptomycin Not assoc w R