TB-Profiler result

Run: SRR13861234
Summary

Run ID: SRR13861234

Sample name:

Date: 2024-04-15T02:58:32.204509

Number of reads: 2550032

Percentage reads mapped: 42.54

Median coverage: 84.0

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 p.Gly234Glu Uncertain significance Mutation from literature
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 2155411 p.Gly234Glu missense_variant 1.0 isoniazid Uncertain significance 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
Rv0010c 13524 p.Gly12Ala missense_variant 1.0 isoniazid
mshA 576259 c.912C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 620690 p.Val267Glu missense_variant 1.0 capreomycin
amikacin
kanamycin
Rv0565c 657622 c.-152G>A upstream_gene_variant 0.99 ethionamide
rpoB 759805 c.-2T>C upstream_gene_variant 0.99 rifampicin
rpoB 761961 p.Pro719Thr missense_variant 1.0 rifampicin
rpoC 764895 p.Ile509Thr missense_variant 1.0 rifampicin
mmpL5 777574 p.Phe303Leu missense_variant 1.0 clofazimine
bedaquiline
mmpL5 777578 c.903C>G synonymous_variant 1.0 clofazimine
bedaquiline
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 801169 p.Lys121* stop_gained 1.0 linezolid
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.1 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1918432 p.Pro165Thr missense_variant 1.0 capreomycin
ndh 2101769 p.Arg425His missense_variant 0.99 ethionamide
delamanid
isoniazid Uncertain significance
katG 2155508 p.Ala202Ser missense_variant 1.0 isoniazid Uncertain significance
pncA 2289474 c.-233C>G upstream_gene_variant 1.0 pyrazinamide
folC 2746862 p.Leu246Arg missense_variant 1.0 para-aminosalicylic_acid
folC 2747268 p.Asp111His missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3065109 c.1083A>G synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
whiB7 3569222 c.-543G>A upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
lpqB 3624508 p.Ile135Val missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625247 p.Arg456Pro missense_variant 1.0 bedaquiline
rifampicin
clpC1 4038468 p.Asp746Gly missense_variant 1.0 pyrazinamide
clpC1 4040148 p.Lys186Ile missense_variant 1.0 pyrazinamide
embC 4240125 p.Cys88Tyr missense_variant 0.99 ethambutol
ethR 4327643 p.Thr32Ile missense_variant 1.0 ethionamide