TB-Profiler result

Run: SRR13837521
Summary

Run ID: SRR13837521

Sample name:

Date: 2024-10-03T20:34:29.886695

Number of reads: 595077

Percentage reads mapped: 97.22

Median coverage: 20.0

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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn c.4_5insA 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
ddn 3986847 c.4_5insA frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fgd1 490804 p.Tyr8Asn missense_variant 1.0 pretomanid
delamanid
clofazimine
fgd1 490893 c.111C>T synonymous_variant 0.93 pretomanid
delamanid
clofazimine
mshA 575498 p.Ala51Pro missense_variant 1.0 isoniazid
ethionamide
Rv0565c 656747 p.Val242Ile missense_variant 1.0 ethionamide
Rv0565c 656828 p.Tyr215His missense_variant 1.0 ethionamide
rpoC 763663 c.294C>A synonymous_variant 1.0 rifampicin
rpoC 763955 p.Lys196Gln missense_variant 0.97 rifampicin
rpoC 765682 p.Asn771Lys missense_variant 0.94 rifampicin
rpoC 766342 c.2973C>A synonymous_variant 1.0 rifampicin
rpsL 781579 p.Leu7Arg missense_variant 1.0 streptomycin
Rv1129c 1254119 p.Ser139Phe missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1416509 p.Arg280Pro missense_variant 1.0 ethambutol
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
inhA 1674315 c.114C>G synonymous_variant 1.0 isoniazid
ethionamide
katG 2154959 c.1153C>A synonymous_variant 1.0 isoniazid
PPE35 2170236 c.376_377insG frameshift_variant 1.0 pyrazinamide Uncertain significance
pncA 2290061 c.-820C>T upstream_gene_variant 1.0 pyrazinamide
folC 2747798 c.-200A>T upstream_gene_variant 1.0 para-aminosalicylic_acid
pepQ 2860252 p.Thr56Ser missense_variant 1.0 bedaquiline
clofazimine
Rv2680 2996652 p.Val183Ala missense_variant 1.0 capreomycin
Rv2752c 3065651 p.Arg181Gly missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448855 p.Val118Ile missense_variant 1.0 ethionamide
whiB7 3569074 c.-395A>G upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
mtrB 3626557 p.Met19Ile missense_variant 1.0 rifampicin
bedaquiline
mtrB 3626629 c.-17_-16insT upstream_gene_variant 1.0 rifampicin
bedaquiline
rpoA 3877765 p.Ala248Gly missense_variant 1.0 rifampicin
panD 4044948 c.-667A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247059 c.546C>G synonymous_variant 1.0 ethambutol
embB 4247144 p.Ser211Pro missense_variant 1.0 ethambutol
ubiA 4269553 p.Ala94Gly missense_variant 1.0 ethambutol
gid 4408259 c.-57G>C upstream_gene_variant 1.0 streptomycin