TB-Profiler result

Run: SRR5818446
Summary

Run ID: SRR5818446

Sample name:

Date: 2024-04-15T08:11:53.809522

Number of reads: 890191

Percentage reads mapped: 98.57

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.442_444delAACinsCA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
mmpR5 779431 c.442_444delAACinsCA frameshift_variant&missense_variant 0.96 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.22 streptomycin 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
gyrB 6454 c.1215C>T synonymous_variant 0.98 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6721 c.1482C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 779283 c.-803G>A upstream_gene_variant 0.97 clofazimine
bedaquiline
mmpL5 779295 c.-815A>G upstream_gene_variant 0.97 clofazimine
bedaquiline
mmpL5 779472 c.-992G>A upstream_gene_variant 0.97 clofazimine
bedaquiline
mmpS5 779523 c.-618T>A upstream_gene_variant 0.97 clofazimine
bedaquiline
mmpS5 779538 c.-633A>C upstream_gene_variant 0.95 clofazimine
bedaquiline
mmpS5 779539 c.-634C>A upstream_gene_variant 0.94 clofazimine
bedaquiline
rplC 801267 c.459A>G synonymous_variant 0.98 linezolid Not assoc w R - Interim
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472313 n.468delGinsAA non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472332 n.487A>G non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472333 n.488G>A non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674816 c.615T>C synonymous_variant 0.99 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
pncA 2289104 c.138A>G synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
embB 4247590 c.1077A>G synonymous_variant 0.96 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.97 ethambutol Not assoc w R
embB 4247815 c.1302C>T synonymous_variant 0.95 ethambutol Not assoc w R - Interim
ethA 4326463 c.1011C>T synonymous_variant 0.99 ethionamide Not assoc w R - Interim
ethA 4326740 p.Arg245His missense_variant 0.98 ethionamide Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R