TB-Profiler result

Run: SRR13861261
Summary

Run ID: SRR13861261

Sample name:

Date: 2024-10-04T11:43:39.166823

Number of reads: 667954

Percentage reads mapped: 33.43

Median coverage: 23.0

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 fbiB c.743delC 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
fbiB 3642276 c.743delC 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
Rv0565c 656172 p.Lys433Asn missense_variant 1.0 ethionamide
nusG 733874 c.-379delC upstream_gene_variant 1.0 rifampicin
nusG 734570 p.Pro106His missense_variant 1.0 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.17 rifampicin
rpoB 760418 c.612G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760514 c.708C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.19 rifampicin Uncertain significance
rpoC 762698 c.-672C>T upstream_gene_variant 1.0 rifampicin
rpoB 762958 p.Leu1051Pro missense_variant 0.87 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.32 rifampicin
rpoC 764434 c.1065A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.35 rifampicin
fbiC 1302962 p.Ala11Gly missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1303706 p.Leu259Arg missense_variant 0.96 pretomanid
delamanid
clofazimine
fbiC 1305384 c.2454G>T synonymous_variant 0.94 pretomanid
delamanid
clofazimine
sigE 1364465 p.Val18Gly missense_variant 1.0 pyrazinamide
Rv1258c 1406724 p.Gln206Leu missense_variant 1.0 streptomycin
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416800 p.Ala183Gly missense_variant 1.0 ethambutol
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833555 p.Thr5Ser missense_variant 0.96 pyrazinamide
rpsA 1834073 p.Lys178* stop_gained 0.78 pyrazinamide Uncertain significance
rpsA 1834222 c.681T>C synonymous_variant 0.32 pyrazinamide
tsnR 1853807 p.Val68Leu missense_variant 1.0 linezolid
bacA 2064191 p.Thr180Ala missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2167669 p.Phe982Leu missense_variant 1.0 pyrazinamide
Rv2681 2996984 c.246C>G synonymous_variant 1.0 capreomycin
Rv2681 2997866 p.Asp376Glu missense_variant 1.0 capreomycin
Rv2752c 3066234 c.-43G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
lpqB 3624242 c.669A>C synonymous_variant 1.0 rifampicin
bedaquiline
rpoA 3878111 p.Lys133Gln missense_variant 0.91 rifampicin
embA 4242703 c.-530C>T upstream_gene_variant 1.0 ethambutol
embB 4249144 c.2631G>C synonymous_variant 1.0 ethambutol