TB-Profiler result

Run: ERR10748563

Summary

Run ID: ERR10748563

Sample name:

Date: 2024-10-05T09:41:56.766835

Number of reads: 2811422

Percentage reads mapped: 99.26

Median coverage: 88.0

Strain: lineage2.2.1;lineage4.1.1.3;lineage4.3.2.1

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 0.17
lineage2 East-Asian RD105 0.54
lineage4.3.2 Euro-American (LAM) None 0.18
lineage4.1 Euro-American None 0.26
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.51
lineage4.1.1.3 Euro-American (X-type) RD193 0.26
lineage4.3.2.1 Euro-American (LAM) RD761 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.56
lineage4 Euro-American None 0.47
lineage4.1.1 Euro-American (X-type) None 0.26
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ile194Thr Uncertain significance Mutation from literature
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Asp8Asn Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
ethR p.Ala95Thr 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
rpoB 761155 p.Ser450Leu missense_variant 0.72 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.5 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.44 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674782 p.Ile194Thr missense_variant 0.5 ethionamide Uncertain significance Mutation from literature
isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid Assoc w R High-level resistance
pncA 2289220 p.Asp8Asn missense_variant 0.46 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 0.44 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
gyrB 5520 p.Pro94Leu missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.28 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.6 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.6 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.46 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.56 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.6 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.27 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.55 rifampicin Not assoc w R
rpoC 763555 c.186C>T synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.31 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 0.46 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.55 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 778979 c.-74G>T upstream_gene_variant 0.61 bedaquiline Not assoc w R - Interim
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781435 c.-125G>C upstream_gene_variant 0.27 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.2 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.53 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.3 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.47 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917818 c.-122C>T upstream_gene_variant 0.13 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.54 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.65 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
pncA 2288856 p.Asp129Ala missense_variant 0.17 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63 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 0.56 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877956 p.Glu184Asp missense_variant 0.23 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.3 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.46 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.24 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.55 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 4407588 c.615A>G synonymous_variant 0.53 streptomycin Not assoc w R
gid 4407798 c.405G>T synonymous_variant 0.22 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.6 streptomycin Not assoc w R
gid 4407973 p.Val77Ala missense_variant 0.14 streptomycin Uncertain significance
gid 4408150 p.Leu18Pro missense_variant 0.27 streptomycin
gid 4408156 p.Leu16Arg missense_variant 0.16 streptomycin Not assoc w R