TB-Profiler result

Run: SRR5818459
Summary

Run ID: SRR5818459

Sample name:

Date: 2024-10-03T18:54:33.067968

Number of reads: 330454

Percentage reads mapped: 88.73

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 p.Ala36Val Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Ala36Val Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. 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 779096 p.Ala36Val missense_variant 0.22 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.69 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 0.76 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6721 c.1482C>T synonymous_variant 0.74 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
rpoB 760461 p.Arg219Cys missense_variant 0.24 rifampicin Uncertain significance
mmpL5 779283 c.-803G>A upstream_gene_variant 0.4 bedaquiline
clofazimine
mmpL5 779295 c.-815A>G upstream_gene_variant 0.41 bedaquiline
clofazimine
mmpR5 779431 p.Asn148Gln missense_variant 0.34 bedaquiline
clofazimine
mmpL5 779472 c.-992G>A upstream_gene_variant 0.32 bedaquiline
clofazimine
mmpS5 779523 c.-618T>A upstream_gene_variant 0.35 bedaquiline
clofazimine
mmpS5 779538 c.-633A>C upstream_gene_variant 0.38 bedaquiline
clofazimine
mmpS5 779539 c.-634C>A upstream_gene_variant 0.38 bedaquiline
clofazimine
rplC 801267 c.459A>G synonymous_variant 0.51 linezolid Not assoc w R - Interim
rrs 1472119 n.274G>A non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472286 n.441C>A non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472297 n.453_461delGTCCGGGTT non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472309 n.464C>T non_coding_transcript_exon_variant 0.91 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472311 n.466C>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472312 n.468_470delGAT non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472328 n.483G>T non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472330 n.485G>T non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.51 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472447 n.602C>T non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472450 n.605A>G non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472451 n.606C>G non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472485 n.640delGinsTA non_coding_transcript_exon_variant 0.6 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.84 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472673 n.828_842delTTTCCTTCCTTGGGAinsGGACATTCCACGTTT non_coding_transcript_exon_variant 0.71 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.68 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475995 n.2338G>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373_2377delACCTCinsGCATG non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1476113 n.2456T>G non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476507 n.2850C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
inhA 1674816 c.615T>C synonymous_variant 0.88 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
tlyA 1917812 c.-128G>A upstream_gene_variant 0.65 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918200 c.261G>A synonymous_variant 0.39 capreomycin Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.28 pyrazinamide Not assoc w R
pncA 2289104 c.138A>G synonymous_variant 0.71 pyrazinamide Not assoc w R - Interim
embB 4247590 c.1077A>G synonymous_variant 0.98 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.98 ethambutol Not assoc w R
embB 4247815 c.1302C>T synonymous_variant 0.98 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 0.92 ethionamide Uncertain significance
ethA 4326764 p.Ala237Val missense_variant 0.98 ethionamide
ethA 4326779 p.Thr232Ile missense_variant 0.99 ethionamide
ethA 4327392 p.Pro28Ser missense_variant 1.0 ethionamide
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407886 p.Thr106Ile missense_variant 0.32 streptomycin
gid 4408185 c.18C>T synonymous_variant 0.96 streptomycin Not assoc w R - Interim