TB-Profiler result

Run: SRR19303779
Summary

Run ID: SRR19303779

Sample name:

Date: 2024-10-04T04:15:05.433943

Number of reads: 993913

Percentage reads mapped: 38.96

Median coverage: 28.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) RD219 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 1.0 ethionamide Uncertain significance
rpoC 764537 p.Pro390Val missense_variant 0.35 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.29 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764671 c.1302G>C synonymous_variant 0.17 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 0.18 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764686 c.1317C>T synonymous_variant 0.17 rifampicin
rpoC 764689 c.1320G>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.18 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Lys missense_variant 0.18 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764719 c.1350G>A synonymous_variant 0.16 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254500 p.Thr12Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254580 c.-46C>G upstream_gene_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Not assoc w R
fbiC 1302885 c.-46G>C upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv2752c 3064875 c.1317C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086987 p.Gln56His missense_variant 1.0 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
fbiA 3641477 p.Asp312Gly missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R