TB-Profiler result

Run: SRR13861255

Summary

Run ID: SRR13861255

Sample name:

Date: 2024-10-04T09:42:10.123602

Number of reads: 453194

Percentage reads mapped: 22.68

Median coverage: 15.0

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 embB p.Met482Ile Mutation from literature
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
embB 4247959 p.Met482Ile missense_variant 1.0 ethambutol Mutation from literature
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 491360 p.Ile193Ser missense_variant 1.0 pretomanid
delamanid
clofazimine
mshA 576396 p.Ser350Ile missense_variant 1.0 isoniazid
ethionamide
rpoB 760225 p.Glu140Ala missense_variant 1.0 rifampicin
rpoC 767186 p.Gln1273* stop_gained 0.93 rifampicin
rplC 800933 p.Pro42His missense_variant 1.0 linezolid
fbiC 1305306 c.2376A>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.63 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 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1918560 c.621G>T synonymous_variant 1.0 capreomycin
bacA 2063120 c.1609C>T synonymous_variant 1.0 kanamycin
capreomycin
streptomycin Not assoc w R - Interim
amikacin
ndh 2102402 p.Leu214Arg missense_variant 1.0 isoniazid Uncertain significance
delamanid
ethionamide
katG 2156175 c.-64T>G upstream_gene_variant 1.0 isoniazid
PPE35 2170540 p.Leu25Val missense_variant 1.0 pyrazinamide
pncA 2288999 p.Phe81Leu missense_variant 1.0 pyrazinamide
fbiD 3339660 c.543C>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0 pyrazinamide
fbiA 3640219 c.-324C>T upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
embA 4244119 p.Tyr296Phe missense_variant 1.0 ethambutol
embB 4247417 p.Tyr302Asn missense_variant 1.0 ethambutol
embB 4248036 p.Val508Gly missense_variant 1.0 ethambutol
embB 4248325 c.1812G>C synonymous_variant 1.0 ethambutol
aftB 4267894 p.Ile315Phe missense_variant 1.0 ethambutol
ethA 4327388 p.Thr29Ile missense_variant 0.95 ethionamide
ethR 4328162 p.His205Pro missense_variant 1.0 ethionamide
whiB6 4338518 c.4C>A synonymous_variant 1.0 kanamycin
capreomycin
amikacin