TB-Profiler result

Run: ERR027453
Summary

Run ID: ERR027453

Sample name:

Date: 2024-10-03T15:06:14.831383

Number of reads: 3481307

Percentage reads mapped: 99.8

Median coverage: 45.0

Strain: lineage2.2.1;lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.25
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage4 Euro-American None 0.78
lineage4.9 Euro-American (H37Rv-like) None 0.76
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
p.Glu761Asp Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide
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 7570 p.Ala90Val missense_variant 0.2 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.43 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.31 rifampicin Uncertain significance Mutation from literature
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.37 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.35 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.36 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 7585 p.Ser95Thr missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.29 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.43 pretomanid
delamanid Not assoc w R - Interim
clofazimine 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
rpoB 763031 c.3225T>C synonymous_variant 0.55 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.27 rifampicin Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23 bedaquiline
clofazimine
rplC 801334 p.Thr176Ala missense_variant 0.21 linezolid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 0.27 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.27 isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.26 rifampicin Not assoc w R
bedaquiline Uncertain significance
whiB6 4338563 c.-42G>T upstream_gene_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.24 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.27 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.23 streptomycin Not assoc w R