TB-Profiler result

Run: d66b56c0-bb7c-4c89-a4e4-c3ba5b288441
Summary

Run ID: d66b56c0-bb7c-4c89-a4e4-c3ba5b288441

Sample name:

Date: 08-10-2023 13:18:12

Number of reads: 714107

Percentage reads mapped: 99.42

Median coverage: 12

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 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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
gyrB 5481 p.Gly81Asp missense_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 5738 p.Thr167Ala missense_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6089 p.Gly284Arg missense_variant 0.2 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6574 c.-728C>T upstream_gene_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491169 c.387C>T synonymous_variant 0.12 delamanid
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 760323 c.517C>T synonymous_variant 0.2 rifampicin
rpoB 760891 p.Asp362Gly missense_variant 0.15 rifampicin
rpoB 762804 p.Gly1000Ser missense_variant 0.17 rifampicin
rpoB 763233 p.Glu1143Lys missense_variant 0.11 rifampicin
rpoC 764214 p.Arg282Gln missense_variant 0.13 rifampicin Uncertain significance
rpoC 764248 c.879C>T synonymous_variant 0.11 rifampicin
rpoC 764254 c.885G>A synonymous_variant 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 775841 c.2640G>T synonymous_variant 0.13 clofazimine
bedaquiline
mmpL5 777749 c.732C>T synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 777965 c.516C>T synonymous_variant 0.18 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1303184 p.Ser85Asn missense_variant 0.12 delamanid
fbiC 1303610 p.Gly227Val missense_variant 0.12 delamanid
fbiC 1304174 p.Val415Ala missense_variant 0.12 delamanid
fbiC 1304282 p.Ala451Val missense_variant 0.18 delamanid
embR 1416717 c.631C>T synonymous_variant 0.12 ethambutol
embR 1417394 c.-47C>T upstream_gene_variant 0.13 ethambutol
rrl 1473985 n.328A>G non_coding_transcript_exon_variant 0.15 linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
rpsA 1834799 p.Glu420Lys missense_variant 0.11 pyrazinamide
rpsA 1834940 p.Asp467Asn missense_variant 0.14 pyrazinamide
tlyA 1917781 c.-159G>A upstream_gene_variant 0.11 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
tlyA 1918248 c.309T>C synonymous_variant 0.13 capreomycin
tlyA 1918314 c.375T>C synonymous_variant 0.2 capreomycin
tlyA 1918640 p.Ser234Leu missense_variant 0.14 capreomycin
ndh 2101853 p.Leu397Pro missense_variant 0.12 ethionamide
isoniazid
katG 2155072 p.Pro347His missense_variant 0.1 isoniazid
katG 2156167 c.-56T>A upstream_gene_variant 0.18 isoniazid
katG 2156421 c.-310G>A upstream_gene_variant 0.13 isoniazid
PPE35 2167717 c.2896T>C synonymous_variant 0.2 pyrazinamide
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168303 c.2310G>A synonymous_variant 0.17 pyrazinamide
PPE35 2168456 c.2157C>T synonymous_variant 0.12 pyrazinamide
PPE35 2169564 p.Gly350Val missense_variant 0.17 pyrazinamide
PPE35 2169896 c.717C>T synonymous_variant 0.13 pyrazinamide
Rv1979c 2222289 c.876C>T synonymous_variant 0.18 clofazimine
bedaquiline
Rv1979c 2223008 c.157T>C synonymous_variant 0.18 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
eis 2714396 p.Glu313Lys missense_variant 0.12 kanamycin
amikacin
ahpC 2726252 c.60C>T synonymous_variant 0.15 isoniazid
ahpC 2726438 c.246C>T synonymous_variant 0.13 isoniazid
folC 2747725 c.-127C>T upstream_gene_variant 0.14 para-aminosalicylic_acid
pepQ 2859601 c.817delG frameshift_variant 0.17 clofazimine
bedaquiline
pepQ 2859617 p.Ala268Thr missense_variant 0.14 clofazimine
bedaquiline
pepQ 2860268 p.Asp51Asn missense_variant 0.1 clofazimine
bedaquiline
pepQ 2860392 c.27G>A synonymous_variant 0.18 clofazimine
bedaquiline
ribD 2986700 c.-139C>T upstream_gene_variant 0.1 para-aminosalicylic_acid
ribD 2987092 p.Val85Ala missense_variant 0.13 para-aminosalicylic_acid
ribD 2987126 c.288C>T synonymous_variant 0.2 para-aminosalicylic_acid
thyA 3074092 p.Arg127His missense_variant 0.13 para-aminosalicylic_acid
thyA 3074350 p.Gly41Asp missense_variant 0.13 para-aminosalicylic_acid
ald 3086673 c.-147G>A upstream_gene_variant 0.15 cycloserine
ald 3087872 c.1053G>A synonymous_variant 0.2 cycloserine
Rv3083 3449592 c.1089C>T synonymous_variant 0.18 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3640848 c.-687C>T upstream_gene_variant 0.17 delamanid
fbiA 3641058 p.Trp172* stop_gained 0.2 delamanid
fbiA 3641428 p.Ala296Thr missense_variant 0.12 delamanid
fbiB 3642111 p.Ala193Thr missense_variant 0.2 delamanid
fbiB 3642812 c.1278C>T synonymous_variant 0.1 delamanid
alr 3840535 p.Gly296Arg missense_variant 0.18 cycloserine
alr 3840733 p.Glu230Lys missense_variant 0.13 cycloserine
rpoA 3877555 p.Ser318Leu missense_variant 0.13 rifampicin Uncertain significance
rpoA 3877888 p.Ala207Val missense_variant 0.12 rifampicin Uncertain significance
clpC1 4039267 p.Asp480Asn missense_variant 0.2 pyrazinamide
embC 4239733 c.-130A>G upstream_gene_variant 0.12 ethambutol
embC 4239940 c.78C>T synonymous_variant 0.13 ethambutol
embC 4241598 p.Met579Thr missense_variant 0.15 ethambutol
embC 4241931 p.Thr690Ile missense_variant 0.15 ethambutol Uncertain significance
embC 4241964 p.Ala701Asp missense_variant 0.12 ethambutol
embC 4242202 c.2340C>T synonymous_variant 0.2 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
embA 4244385 p.Ile385Phe missense_variant 0.15 ethambutol
embA 4244647 p.Arg472Gln missense_variant 0.12 ethambutol
embA 4244930 c.1703_1706delCCAA frameshift_variant 0.12 ethambutol
embB 4247150 p.Arg213Trp missense_variant 0.2 ethambutol Uncertain significance
embB 4249009 c.2496G>A synonymous_variant 0.14 ethambutol
embB 4249104 p.Leu864Pro missense_variant 0.11 ethambutol
embB 4249784 p.Pro1091Ser missense_variant 0.17 ethambutol
aftB 4267140 p.Leu566Gln missense_variant 0.12 capreomycin
amikacin
ubiA 4268962 p.Trp291* stop_gained 0.2 ethambutol
ethA 4326090 p.Leu462Ile missense_variant 0.2 ethionamide
ethR 4327096 c.-453G>A upstream_gene_variant 0.11 ethionamide
ethR 4327708 p.Ala54Thr missense_variant 1.0 ethionamide
ethA 4327881 c.-408G>A upstream_gene_variant 0.14 ethionamide
whiB6 4338329 p.Asp65Asn missense_variant 0.12 streptomycin
capreomycin
amikacin
gid 4407620 p.Tyr195His missense_variant 1.0 streptomycin Uncertain significance
gid 4407669 p.Met178Ile missense_variant 0.15 streptomycin Uncertain significance
gid 4408295 c.-93G>A upstream_gene_variant 0.12 streptomycin