TB-Profiler result

Run: SRR1048988
Summary

Run ID: SRR1048988

Sample name:

Date: 2024-04-14T12:43:31.871430

Number of reads: 225415

Percentage reads mapped: 7.32

Median coverage: 5.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.31
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.55
lineage2.2 East-Asian (Beijing) RD105;RD207 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.421_423delTTGinsCC Assoc w R High-level resistance
p.Ser140Asn 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 2155689 c.421_423delTTGinsCC frameshift_variant&missense_variant 0.67 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.65 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
rpoC 762980 c.-390T>C upstream_gene_variant 0.6 rifampicin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.73 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.65 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.94 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
katG 2155600 p.Cys171Val missense_variant 0.6 isoniazid
katG 2155613 p.Phe167Leu missense_variant 0.64 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.64 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.69 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.71 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.7 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.7 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.61 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.62 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.65 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.66 isoniazid
katG 2155704 c.408C>T synonymous_variant 0.65 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.63 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.62 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.61 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.59 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.62 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.62 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.62 isoniazid
katG 2155765 p.His116Thr missense_variant 0.59 isoniazid