TB-Profiler result

Run: ERR4814402
Summary

Run ID: ERR4814402

Sample name:

Date: 20-10-2023 07:32:18

Number of reads: 3783332

Percentage reads mapped: 99.56

Strain: lineage4.8;lineage3

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.45
lineage4 Euro-American LAM;T;S;X;H None 0.53
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.57
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.46
gyrA 9304 p.Gly668Asp missense_variant 0.5
gyrA 9596 c.2295G>T synonymous_variant 0.46
gyrA 9777 p.Asn826Asp missense_variant 0.47
fgd1 491742 c.960T>C synonymous_variant 0.39
rpoB 759746 c.-61C>T upstream_gene_variant 0.38
rpoB 760975 p.Met390Thr missense_variant 0.48
rpoC 762434 c.-936T>G upstream_gene_variant 0.5
rpoB 762636 p.Lys944Glu missense_variant 0.41
rpoC 763031 c.-339T>C upstream_gene_variant 0.34
rpoC 764181 p.Asp271Gly missense_variant 0.52
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.56
rrl 1475090 n.1433A>C non_coding_transcript_exon_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.41
PPE35 2167926 p.Leu896Ser missense_variant 0.33
PPE35 2168149 p.Pro822Ser missense_variant 0.55
PPE35 2170769 c.-157C>T upstream_gene_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.46
pncA 2289365 c.-125delC upstream_gene_variant 0.52
eis 2714784 c.549C>T synonymous_variant 0.45
eis 2714915 c.418C>T synonymous_variant 0.44
eis 2715432 c.-100C>T upstream_gene_variant 0.43
ahpC 2726105 c.-88G>A upstream_gene_variant 0.44
ald 3086767 c.-53A>C upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 0.49
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.42
rpoA 3877752 c.756C>T synonymous_variant 0.44
embC 4242075 p.Arg738Gln missense_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244990 c.1758G>C synonymous_variant 0.48
aftB 4267715 c.1122G>A synonymous_variant 0.68
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.37