TB-Profiler result

Run: SRR13861315
Summary

Run ID: SRR13861315

Sample name:

Date: 2024-10-05T14:21:20.748350

Number of reads: 904020

Percentage reads mapped: 30.16

Median coverage: 31.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
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
dnaA 335 p.Thr112Ser missense_variant 1.0 isoniazid
gyrB 6406 p.Asn389Lys missense_variant 1.0 levofloxacin
moxifloxacin
mshA 575880 p.His178Pro missense_variant 1.0 isoniazid
ethionamide
mshA 576356 p.Ala337Ser missense_variant 1.0 isoniazid
ethionamide
mmaA3 738203 c.-54T>C upstream_gene_variant 1.0 isoniazid
Rv1129c 1254144 p.Thr131Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1303517 p.Met196Arg missense_variant 1.0 pretomanid
delamanid
clofazimine
rrl 1473558 n.-100T>G upstream_gene_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1673792 c.-410G>T upstream_gene_variant 1.0 isoniazid
ethionamide
rpsA 1833709 c.168C>T synonymous_variant 1.0 pyrazinamide
rpsA 1834448 p.Lys303* stop_gained 1.0 pyrazinamide Uncertain significance
tlyA 1917605 c.-335G>T upstream_gene_variant 1.0 capreomycin
tlyA 1918103 p.Val55Ala missense_variant 1.0 capreomycin
tlyA 1918250 p.Gly104Ala missense_variant 1.0 capreomycin
bacA 2064591 c.138C>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
katG 2156538 c.-427A>T upstream_gene_variant 1.0 isoniazid
Rv1979c 2222544 c.621G>A synonymous_variant 1.0 bedaquiline
clofazimine
eis 2715078 c.255C>G synonymous_variant 1.0 kanamycin
amikacin
folC 2747750 c.-152G>C upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv2680 2995806 c.-299_-298insC upstream_gene_variant 1.0 capreomycin
ald 3086982 p.Ala55Pro missense_variant 1.0 cycloserine
Rv3083 3449935 p.Ile478Val missense_variant 1.0 ethionamide
whiB7 3569257 c.-578A>G upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
lpqB 3623916 p.Arg332Gln missense_variant 1.0 rifampicin
bedaquiline
mtrB 3627581 c.-968G>A upstream_gene_variant 1.0 rifampicin
bedaquiline
fbiB 3642147 p.Val205Phe missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3642189 p.Gly219Trp missense_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4039120 p.Ser529Ala missense_variant 1.0 pyrazinamide
clpC1 4039306 p.Gln467Lys missense_variant 0.97 pyrazinamide
clpC1 4039400 c.1304delA frameshift_variant 1.0 pyrazinamide
embC 4239311 c.-552G>C upstream_gene_variant 1.0 ethambutol
ethA 4327034 p.Tyr147Phe missense_variant 1.0 ethionamide
gid 4408038 p.Ile55Met missense_variant 1.0 streptomycin