TB-Profiler result

Run: SRR13861249
Summary

Run ID: SRR13861249

Sample name:

Date: 2024-03-26T17:00:49.380957

Number of reads: 857727

Percentage reads mapped: 42.93

Median coverage: 29.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG c.1313_1314insT Assoc w R High-level resistance
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
katG 2154798 c.1313_1314insT frameshift_variant 1.0 isoniazid Assoc w R High-level 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
gyrB 5906 p.Val223Leu missense_variant 1.0 levofloxacin
moxifloxacin
gyrB 6011 p.Val258Met missense_variant 1.0 levofloxacin
moxifloxacin
gyrB 6678 p.Pro480Arg missense_variant 1.0 levofloxacin
moxifloxacin
fgd1 490676 c.-107G>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
ccsA 620028 c.138G>C synonymous_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 759638 c.-169T>A upstream_gene_variant 1.0 rifampicin
rpoB 760454 c.650delG frameshift_variant 1.0 rifampicin
rpoC 765487 p.Met706Ile missense_variant 1.0 rifampicin
rpsL 781409 c.-151T>A upstream_gene_variant 1.0 streptomycin
Rv1129c 1254013 p.Met174Ile missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254452 p.Glu28Ala missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063125 p.Ala535Asp missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2064843 c.-115C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2154654 p.Ser486Arg missense_variant 1.0 isoniazid
katG 2154882 c.1230G>A synonymous_variant 1.0 isoniazid
katG 2155857 c.255C>A synonymous_variant 0.97 isoniazid
PPE35 2170198 p.Ala139Ser missense_variant 1.0 pyrazinamide
pncA 2290069 c.-828C>T upstream_gene_variant 1.0 pyrazinamide
eis 2714922 c.411G>A synonymous_variant 1.0 amikacin
kanamycin
thyA 3074067 c.405C>G synonymous_variant 1.0 para-aminosalicylic_acid
lpqB 3624738 p.Ala58Val missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625436 p.Ile393Asn missense_variant 1.0 bedaquiline
rifampicin
mtrA 3626728 p.Asp208Tyr missense_variant 1.0 bedaquiline
rifampicin
alr 3840223 c.1198A>C synonymous_variant 1.0 cycloserine
alr 3840711 p.Ser237Leu missense_variant 1.0 cycloserine
clpC1 4039648 p.Glu353Gln missense_variant 1.0 pyrazinamide
embC 4242023 p.Val721Leu missense_variant 1.0 ethambutol
embA 4245071 c.1839G>A synonymous_variant 1.0 ethambutol
ethA 4327364 p.Lys37Arg missense_variant 1.0 ethionamide