TB-Profiler result

Run: ERR2512786
Summary

Run ID: ERR2512786

Sample name:

Date: 20-10-2023 12:39:29

Number of reads: 4393258

Percentage reads mapped: 99.67

Strain: lineage4.7;lineage4.1.2.1

Drug-resistance: Other

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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 R embB p.Met306Ile (0.49)
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.5
lineage4.7 Euro-American (mainly T) T1;T5 None 0.52
lineage4.1.2 Euro-American T;H None 0.45
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.46
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
embB 4247431 p.Met306Ile missense_variant 0.49 ethambutol
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 0.49
gyrA 8571 p.Leu424Val missense_variant 0.52
gyrA 9304 p.Gly668Asp missense_variant 0.49
fgd1 491591 p.Lys270Met missense_variant 0.49
mshA 575679 p.Asn111Ser missense_variant 0.52
rpoB 760115 c.309C>T synonymous_variant 0.42
rpoC 765150 p.Gly594Glu missense_variant 0.39
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781800 c.241C>T synonymous_variant 0.51
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.49
inhA 1673472 c.-730C>T upstream_gene_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169413 c.1200T>C synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 0.48
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.46
embB 4249732 c.3219C>G synonymous_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0