TB-Profiler result

Run: ERR245716
Summary

Run ID: ERR245716

Sample name:

Date: 2024-07-11T12:48:58.799588

Number of reads: 5766812

Percentage reads mapped: 94.88

Median coverage: 92.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.99 ethionamide Uncertain significance
rpoB 761312 c.1506G>C synonymous_variant 0.12 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 764554 c.1185C>T synonymous_variant 0.11 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.12 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765580 c.2211G>C synonymous_variant 0.14 rifampicin
rpoC 765631 p.Asp754Glu missense_variant 0.12 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.12 rifampicin
rpoC 765883 c.2514C>G synonymous_variant 0.11 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 766408 c.3039C>G synonymous_variant 0.12 rifampicin
rpoC 766411 c.3042C>G synonymous_variant 0.11 rifampicin
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 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781832 c.273T>C synonymous_variant 0.14 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.14 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.14 streptomycin
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 1473756 n.99G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
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
ndh 2103226 c.-184C>G upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
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
thyX 3067601 c.345G>C synonymous_variant 0.11 para-aminosalicylic_acid
ald 3086739 c.-81G>A upstream_gene_variant 0.99 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3627167 c.-554T>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3627182 c.-569T>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
rpoA 3877553 p.Glu319Gln missense_variant 0.12 rifampicin
clpC1 4038596 c.2109A>G synonymous_variant 0.13 pyrazinamide
embC 4240789 c.927T>C synonymous_variant 0.12 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4242754 c.-479G>C upstream_gene_variant 0.14 ethambutol
embC 4242764 p.Val968Leu missense_variant 0.13 ethambutol
embA 4243460 c.228C>T synonymous_variant 0.99 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_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
gid 4407927 p.Glu92Asp missense_variant 0.99 streptomycin Not assoc w R