TB-Profiler result

Run: SRR1048981
Summary

Run ID: SRR1048981

Sample name:

Date: 2024-04-14T19:19:42.601250

Number of reads: 493163

Percentage reads mapped: 14.61

Median coverage: 10.0

Strain: lineage3

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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 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 0.67 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.65 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
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
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764338 p.Glu323Asp missense_variant 0.5 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.57 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.57 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.6 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.5 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.52 rifampicin
rpoC 764398 c.1029G>C synonymous_variant 0.52 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.55 rifampicin
rpoC 764410 c.1041G>T synonymous_variant 0.52 rifampicin
Rv1129c 1254549 c.-15G>A upstream_gene_variant 0.88 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417434 c.-87T>C upstream_gene_variant 1.0 ethambutol
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.53 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155637 p.Leu159Ile missense_variant 0.55 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.55 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.54 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.54 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.58 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.56 isoniazid
katG 2155704 c.408C>T synonymous_variant 0.64 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.64 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.61 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.57 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.53 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.56 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.56 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.56 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin