TB-Profiler result

Run: ERR108438
Summary

Run ID: ERR108438

Sample name:

Date: 2024-10-04T16:11:20.297594

Number of reads: 4336697

Percentage reads mapped: 99.47

Median coverage: 89.0

Strain: lineage2.2.1;lineage4.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.65
lineage2 East-Asian RD105 0.24
lineage4.2 Euro-American None 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.26
lineage2.2 East-Asian (Beijing) RD105;RD207 0.26
lineage4 Euro-American None 0.75
lineage4.2.1 Euro-American (TUR) None 0.06
lineage4.3.3 Euro-American (LAM) RD115 0.63
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
p.Glu761Asp Uncertain significance Mutation from literature
isoniazid inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Asp354Ala Assoc w R
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-7T>C Assoc w R - Interim
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 761109 p.Asp435Tyr missense_variant 0.59 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.28 rifampicin Uncertain significance Mutation from literature
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.18 streptomycin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 0.62 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.32 kanamycin Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.7 ethambutol Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.27 ethambutol Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.16 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
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 0.67 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 0.24 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.31 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.25 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.2 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.17 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.24 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.32 rifampicin Not assoc w R
rpoC 766667 p.Ser1100Ala missense_variant 0.62 rifampicin Uncertain significance
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 0.29 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.28 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32 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 0.29 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 0.34 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32 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 0.3 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
tlyA 1918681 p.Asp248Cys missense_variant 0.58 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.12 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289226 p.Ile6Leu missense_variant 0.21 pyrazinamide Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.63 isoniazid
pepQ 2860571 c.-153T>G upstream_gene_variant 0.61 bedaquiline
clofazimine
thyA 3073868 p.Thr202Ala missense_variant 0.73 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.1 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339490 p.Leu125Ile missense_variant 0.64 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 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 0.43 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.62 pyrazinamide Not assoc w R
glpK 4139842 c.-87T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.4 ethambutol Not assoc w R
embA 4244823 p.Val531Leu missense_variant 0.55 ethambutol Uncertain significance
embB 4248316 c.1803C>T synonymous_variant 0.62 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.1 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.26 ethambutol Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
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 0.23 streptomycin Not assoc w R
gid 4407877 p.Gly109Ala missense_variant 0.73 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.17 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.7 streptomycin Not assoc w R