TB-Profiler result

Run: ERR12328189
Summary

Run ID: ERR12328189

Sample name:

Date: 2024-10-05T13:24:07.272067

Number of reads: 2310762

Percentage reads mapped: 98.57

Median coverage: 72.0

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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764896 c.1527C>T synonymous_variant 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801357 c.549T>C synonymous_variant 0.11 linezolid
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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472031 n.186G>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472032 n.187G>C non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 1.0 pyrazinamide 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
PPE35 2169023 c.1590G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517989 c.-126T>C upstream_gene_variant 0.13 isoniazid
kasA 2518248 p.Ala45Val missense_variant 0.12 isoniazid
kasA 2518255 c.141A>G synonymous_variant 0.12 isoniazid
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 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3626912 c.438T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626930 c.-317A>G upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrA 3626939 p.Glu137Asp missense_variant 0.14 rifampicin
bedaquiline
mtrB 3626942 c.-329A>C upstream_gene_variant 0.12 rifampicin
bedaquiline
rpoA 3877737 c.771G>C synonymous_variant 0.14 rifampicin
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877788 c.720G>A synonymous_variant 0.15 rifampicin
rpoA 3878205 c.303T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.12 rifampicin
rpoA 3878229 c.279C>G synonymous_variant 0.16 rifampicin
rpoA 3878241 c.267G>A synonymous_variant 0.15 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.14 rifampicin Uncertain significance
rpoA 3878304 c.204G>C synonymous_variant 0.12 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
clpC1 4038790 c.1915C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038845 c.1860G>C synonymous_variant 0.16 pyrazinamide
clpC1 4038848 c.1857C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038863 c.1842G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>T synonymous_variant 0.15 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.11 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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
ethA 4326676 p.Ser266Arg missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407595 p.Val203Gly missense_variant 1.0 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R