TB-Profiler result

Run: SRR19303775
Summary

Run ID: SRR19303775

Sample name:

Date: 2024-03-26T17:08:38.277882

Number of reads: 1103329

Percentage reads mapped: 41.56

Median coverage: 32.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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
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
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 8649 p.Arg450Gly missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9367 p.Ala689Gly missense_variant 1.0 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
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 764521 c.1152T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.26 rifampicin
rpoC 764537 p.Pro390Val missense_variant 0.28 rifampicin
rpoC 764540 p.Val391Ile missense_variant 0.32 rifampicin
rpoC 764548 c.1179G>C synonymous_variant 0.3 rifampicin
rpoC 764549 c.1180_1182delCCGinsGC frameshift_variant&missense_variant 0.3 rifampicin
rpoC 764552 p.Gly395Asn missense_variant 0.32 rifampicin
rpoC 764557 p.Asn396Lys missense_variant 0.3 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>C synonymous_variant 0.29 rifampicin
rpoC 764576 p.Ser403Ala missense_variant 0.29 rifampicin Uncertain significance
rpoC 764581 c.1212T>C synonymous_variant 0.28 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.31 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.37 rifampicin
rpoC 764620 c.1251G>C synonymous_variant 0.33 rifampicin
rpoC 764621 c.1252_1254delCTCinsTG frameshift_variant&missense_variant 0.33 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777484 p.Gln333Glu missense_variant 0.97 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
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
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 0.98 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin 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
fbiB 3642877 p.Lys448Arg missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
ddn 3986682 c.-162A>G upstream_gene_variant 1.0 delamanid
pretomanid
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139246 c.510C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R