TB-Profiler result

Run: SRR1048980
Summary

Run ID: SRR1048980

Sample name:

Date: 2024-10-04T09:33:16.489481

Number of reads: 493891

Percentage reads mapped: 14.62

Median coverage: 10.0

Strain: lineage3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.97
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG 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 2155693 p.Ser140Asn missense_variant 0.7 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13642 c.-84A>T upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoC 762893 c.-477C>T upstream_gene_variant 0.33 rifampicin
rpoC 762896 c.-474G>C upstream_gene_variant 0.38 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.35 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.33 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.33 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.47 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.43 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.27 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.26 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.3 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.32 rifampicin
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.32 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>T synonymous_variant 0.33 rifampicin
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1129c 1254549 c.-15G>A upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.6 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.65 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.71 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.63 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.63 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.6 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155600 p.Cys171Val missense_variant 0.62 isoniazid
katG 2155613 p.Phe167Leu missense_variant 0.71 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.67 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.61 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.67 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.71 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.71 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.7 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.7 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.68 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.68 isoniazid
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.72 isoniazid Not assoc w R - Interim
katG 2155704 c.408C>T synonymous_variant 0.71 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.67 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.67 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.67 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.63 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.63 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.63 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.6 isoniazid
katG 2155765 p.His116Thr missense_variant 0.53 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.83 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
clpC1 4038680 c.2025G>A synonymous_variant 1.0 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R