TB-Profiler result

Run: ERR2027220
Summary

Run ID: ERR2027220

Sample name:

Date: 2024-10-05T04:24:12.581255

Number of reads: 362489

Percentage reads mapped: 84.39

Median coverage: 15.0

Strain: lineage3.1.3

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 1.0
lineage3.1.3 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 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 620700 c.810C>G synonymous_variant 1.0 kanamycin
capreomycin
amikacin
hadA 731892 c.-38G>A upstream_gene_variant 1.0 isoniazid
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
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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
atpE 1461186 p.Arg48Trp missense_variant 1.0 bedaquiline
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1474171 n.514C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474280 n.623C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474284 n.631_633delCCT non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474293 n.637_651delCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474317 n.660G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474383 n.726G>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834159 c.618G>A synonymous_variant 1.0 pyrazinamide 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 2222732 c.432delT frameshift_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
folC 2746876 c.723C>T synonymous_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 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
Rv2752c 3065860 p.Leu111Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
alr 3841207 p.His72Tyr missense_variant 1.0 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
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