TB-Profiler result

Run: ERR190343
Summary

Run ID: ERR190343

Sample name:

Date: 2024-10-03T21:48:33.983368

Number of reads: 4299863

Percentage reads mapped: 96.52

Median coverage: 93.0

Strain: lineage3;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.78
lineage4.3 Euro-American (LAM) None 0.16
lineage4 Euro-American None 0.22
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.18
lineage4.3.4 Euro-American (LAM) RD174 0.24
lineage4.3.4.2 Euro-American (LAM) RD174 0.16
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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13250 c.309G>A synonymous_variant 0.81 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.75 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574900 c.-448G>C upstream_gene_variant 0.85 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.73 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.76 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.8 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.81 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.83 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.8 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.82 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2681 2997736 c.1009_1011delCCG conservative_inframe_deletion 0.83 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.96 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.21 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642098 c.564G>A synonymous_variant 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.82 cycloserine
alr 3840719 c.702A>G synonymous_variant 0.17 cycloserine
rpoA 3878622 c.-115C>G upstream_gene_variant 0.83 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
panD 4043938 p.Ile115Thr missense_variant 0.12 pyrazinamide Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.75 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.96 ethambutol Not assoc w R
embA 4245883 p.Gly884Asp missense_variant 0.79 ethambutol 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 0.98 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.78 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.23 streptomycin Not assoc w R