TB-Profiler result

Run: SRR6046834
Summary

Run ID: SRR6046834

Sample name:

Date: 2024-03-25T19:42:41.366383

Number of reads: 26468

Percentage reads mapped: 1.54

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
rpoC 762896 c.-474G>C upstream_gene_variant 0.83 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.94 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.94 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.94 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.94 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.94 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.94 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.93 rifampicin
rpoC 763013 c.-357C>G upstream_gene_variant 0.92 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.92 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.92 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 1.0 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 1.0 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid