TB-Profiler result

Run: SRR13837946
Summary

Run ID: SRR13837946

Sample name:

Date: 2024-10-03T22:35:52.815526

Number of reads: 1469572

Percentage reads mapped: 95.03

Median coverage: 49.5

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide pncA p.Val7Leu Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.827dupC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303756 c.827dupC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pncA 2289223 p.Val7Leu missense_variant 1.0 pyrazinamide 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
gyrB 5850 c.611_612insA frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
mmaA3 737500 p.Ile217Ser missense_variant 1.0 isoniazid
mmaA3 738175 c.-26A>C upstream_gene_variant 1.0 isoniazid
rpoB 762083 c.2277T>A synonymous_variant 1.0 rifampicin
rpoC 766578 p.Asp1070Val missense_variant 1.0 rifampicin
mmpL5 776436 p.Ala682Gly missense_variant 1.0 bedaquiline
clofazimine
fbiC 1304155 p.Arg409Gly missense_variant 1.0 pretomanid
delamanid
clofazimine
atpE 1460879 c.-166C>A upstream_gene_variant 1.0 bedaquiline
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
ndh 2102784 p.Gly87Ser missense_variant 1.0 isoniazid
delamanid
ethionamide
pncA 2290201 c.-960G>A upstream_gene_variant 1.0 pyrazinamide
kasA 2518058 c.-57G>A upstream_gene_variant 1.0 isoniazid
eis 2714947 p.Phe129Ser missense_variant 1.0 kanamycin
amikacin
pepQ 2860319 p.Ser34Thr missense_variant 1.0 bedaquiline
clofazimine
Rv2752c 3064817 p.Asp459Tyr missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
whiB7 3568660 p.Pro7Leu missense_variant 1.0 kanamycin
amikacin
streptomycin Uncertain significance
lpqB 3623509 p.Val468Ile missense_variant 1.0 rifampicin Uncertain significance
bedaquiline
mtrA 3627016 p.Leu112Val missense_variant 1.0 rifampicin
bedaquiline
alr 3841536 c.-117_-116insT upstream_gene_variant 1.0 cycloserine
ddn 3986940 p.Asp33His missense_variant 1.0 pretomanid
delamanid
panD 4045249 c.-968C>G upstream_gene_variant 1.0 pyrazinamide
glpK 4138519 p.Glu413* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embB 4246529 p.Ser6Arg missense_variant 1.0 ethambutol