TB-Profiler result

Run: SRR1049022
Summary

Run ID: SRR1049022

Sample name:

Date: 2024-04-13T22:05:37.467178

Number of reads: 131178

Percentage reads mapped: 4.31

Median coverage: 2.0

Strain: lineage2.2.2;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
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.1
lineage4.9 Euro-American (H37Rv-like) None 0.82
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 1.0 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn 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
rpoC 762893 c.-477C>T upstream_gene_variant 0.6 rifampicin
rpoC 762896 c.-474G>C upstream_gene_variant 0.73 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.75 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.82 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.82 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.75 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.62 rifampicin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.82 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 0.75 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 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.89 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 0.91 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
katG 2155626 c.486G>C synonymous_variant 1.0 isoniazid
katG 2155637 p.Leu159Ile missense_variant 1.0 isoniazid
katG 2155641 p.Lys157Arg missense_variant 1.0 isoniazid
katG 2155650 c.462G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 1.0 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 1.0 isoniazid
katG 2155668 c.444G>C synonymous_variant 1.0 isoniazid