TB-Profiler result

Run: ERR11465112

Summary

Run ID: ERR11465112

Sample name:

Date: 07-01-2024 13:47:50

Number of reads: 6179509

Percentage reads mapped: 99.65

Strain: lineage4.8;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 embA p.Asp4Asn (0.53)
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 0.46
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.5
lineage4.1.2 Euro-American T;H None 0.53
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.49
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
embA 4243242 p.Asp4Asn missense_variant 0.53 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 0.48
gyrA 9304 p.Gly668Asp missense_variant 0.41
fgd1 491591 p.Lys270Met missense_variant 0.44
mshA 575679 p.Asn111Ser missense_variant 0.59
mshA 576108 p.Ala254Gly missense_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 0.53
rpoC 765150 p.Gly594Glu missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303547 p.Pro206Leu missense_variant 0.49
Rv1258c 1406622 p.Leu240Arg missense_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471777 n.-69C>G upstream_gene_variant 0.57
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.56
PPE35 2169356 c.1257C>T synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.52
ald 3086788 c.-32T>C upstream_gene_variant 0.43
ald 3086987 p.Gln56His missense_variant 0.52
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.46
fprA 3474119 p.Met38Thr missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0