TB-Profiler result

Run: SRR13861363
Summary

Run ID: SRR13861363

Sample name:

Date: 2024-04-16T10:51:14.650238

Number of reads: 1529213

Percentage reads mapped: 76.54

Median coverage: 51.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
gyrA 7837 p.Gly179Val missense_variant 1.0 levofloxacin
moxifloxacin
rpoB 762257 c.2451C>G synonymous_variant 1.0 rifampicin
mmpL5 777730 p.Gly251Arg missense_variant 0.98 clofazimine
bedaquiline
fbiC 1304816 p.His629Arg missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304869 p.Leu647Met missense_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1364580 p.Asp56Glu missense_variant 1.0 pyrazinamide
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
tlyA 1917613 c.-327G>T upstream_gene_variant 1.0 capreomycin
tlyA 1918527 c.588G>T synonymous_variant 1.0 capreomycin
bacA 2064771 c.-44delG upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2102259 p.Ser262Ala missense_variant 1.0 ethionamide
delamanid
isoniazid
ndh 2102557 c.485delG frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2156260 c.-149C>A upstream_gene_variant 1.0 isoniazid
PPE35 2169123 p.Thr497Ile missense_variant 1.0 pyrazinamide
Rv2681 2997346 c.609dupG frameshift_variant 1.0 capreomycin Uncertain significance
Rv2752c 3066145 p.Leu16Ser missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv3236c 3612326 p.Thr264Ile missense_variant 1.0 pyrazinamide
Rv3236c 3612504 p.His205Tyr missense_variant 1.0 pyrazinamide
Rv3236c 3612779 p.Leu113* stop_gained 1.0 pyrazinamide Uncertain significance
lpqB 3623745 p.Asp389Gly missense_variant 1.0 bedaquiline
rifampicin
lpqB 3624635 c.275_276insT frameshift_variant 1.0 bedaquiline
rifampicin Uncertain significance
fbiB 3640821 c.-714G>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3878381 p.Leu43Met missense_variant 1.0 rifampicin
rpoA 3878543 c.-36G>C upstream_gene_variant 1.0 rifampicin
embC 4239354 c.-509A>T upstream_gene_variant 1.0 ethambutol
embC 4240536 c.678delC frameshift_variant 1.0 ethambutol
embB 4248562 c.2049G>C synonymous_variant 1.0 ethambutol