TB-Profiler result

Run: ERR2707224

Summary

Run ID: ERR2707224

Sample name:

Date: 19-10-2023 12:00:25

Number of reads: 4649206

Percentage reads mapped: 99.58

Strain: lineage4.6.1.2

Drug-resistance: MDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (0.96)
Isoniazid R katG p.Ser315Thr (0.95)
Ethambutol R embB p.Gly406Ala (0.98)
Pyrazinamide R pncA p.Asp12Ala (0.93)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.140delT (0.97), ethA c.140delT (0.97)
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
lineage4.6 Euro-American T;LAM None 0.96
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.97
lineage4.6.1.2 Euro-American T2 RD724 0.95
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
rpoB 761110 p.Asp435Val missense_variant 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 0.93 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.98 ethambutol
ethA 4327333 c.140delT frameshift_variant 0.97 ethionamide, ethionamide
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 7539 p.Thr80Ala missense_variant 0.94
gyrA 7569 p.Ala90Trp missense_variant 0.96
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764810 p.Pro481Thr missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472983 n.1138A>C non_coding_transcript_exon_variant 0.96
rrl 1475373 n.1716G>A non_coding_transcript_exon_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168631 p.Asn661Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065920 p.Pro91Leu missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987215 c.372A>G synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408093 p.Gly37Val missense_variant 0.99