TB-Profiler result

Run: ERR4830092
Summary

Run ID: ERR4830092

Sample name:

Date: 2024-10-04T21:54:01.544376

Number of reads: 2607502

Percentage reads mapped: 99.66

Median coverage: 81.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.82
lineage2 East-Asian RD105 0.19
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage4 Euro-American None 0.8
lineage4.3.3 Euro-American (LAM) RD115 0.77
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 c.122delA Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Asn379Asp Assoc w R - Interim
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Arg222Gly 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
rpoB 761155 p.Ser450Leu missense_variant 0.29 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid Assoc w R High-level resistance
pncA 2289119 c.122delA frameshift_variant 0.19 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.2 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.22 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.24 ethambutol Assoc w R
ethA 4326339 p.Asn379Asp missense_variant 0.25 ethionamide Assoc w R - Interim
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 1091 p.Ser364Thr missense_variant 0.87 isoniazid Uncertain significance
gyrB 6142 c.903G>C synonymous_variant 0.76 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 8040 p.Gly247Ser missense_variant 0.76 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
gyrA 9752 c.2451C>G synonymous_variant 0.78 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.19 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.16 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.13 ethionamide Uncertain significance
rpoB 761268 p.Ile488Val missense_variant 0.16 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.24 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 0.2 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.14 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2 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 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.25 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476729 n.3072A>G non_coding_transcript_exon_variant 0.78 capreomycin
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.76 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 0.23 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.76 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.21 pyrazinamide 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 2518919 p.Gly269Ser missense_variant 0.76 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.8 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.74 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.14 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 0.18 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641810 c.276G>C synonymous_variant 0.28 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.8 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407927 p.Glu92Asp missense_variant 0.17 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R