TB-Profiler result

Run: SRR13861540
Summary

Run ID: SRR13861540

Sample name:

Date: 2024-04-15T17:19:53.478884

Number of reads: 1073524

Percentage reads mapped: 35.82

Median coverage: 36.0

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
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 clofazimine
bedaquiline
fbiC 1304155 p.Arg409Gly missense_variant 1.0 clofazimine
pretomanid
delamanid
atpE 1460879 c.-166C>A upstream_gene_variant 1.0 bedaquiline
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.64 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
ndh 2102784 p.Gly87Ser missense_variant 1.0 ethionamide
delamanid
isoniazid
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 amikacin
kanamycin
pepQ 2860319 p.Ser34Thr missense_variant 1.0 clofazimine
bedaquiline
Rv2752c 3064817 p.Asp459Tyr missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
whiB7 3568660 p.Pro7Leu missense_variant 1.0 streptomycin Uncertain significance
amikacin
kanamycin
lpqB 3623509 p.Val468Ile missense_variant 1.0 bedaquiline
rifampicin Uncertain significance
mtrA 3627016 p.Leu112Val missense_variant 1.0 bedaquiline
rifampicin
alr 3841536 c.-117_-116insT upstream_gene_variant 1.0 cycloserine
ddn 3986940 p.Asp33His missense_variant 1.0 delamanid
pretomanid
panD 4045249 c.-968C>G upstream_gene_variant 1.0 pyrazinamide
glpK 4138519 p.Glu413* stop_gained 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embB 4246529 p.Ser6Arg missense_variant 1.0 ethambutol