TB-Profiler result

Run: ERR9806867
Summary

Run ID: ERR9806867

Sample name:

Date: 18-05-2023 17:19:06

Number of reads: 2504725

Percentage reads mapped: 99.64

Strain: lineage4.3.2.1

Drug-resistance: Pre-XDR-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.His445Asn (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrB p.Glu501Asp (0.86)
Moxifloxacin R gyrB p.Glu501Asp (0.86)
Ofloxacin R gyrB p.Glu501Asp (0.86)
Levofloxacin R gyrB p.Glu501Asp (0.86)
Ciprofloxacin R gyrB p.Glu501Asp (0.86)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 1.0
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
gyrB 6742 p.Glu501Asp missense_variant 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7451 c.150C>A synonymous_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.96
mshA 575739 p.Ala131Val missense_variant 0.12
rpoB 761279 p.Ile491Met missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765189 p.Pro607Gln missense_variant 0.12
mmpL5 775608 c.2872dupG frameshift_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777229 p.Arg418Cys missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304611 p.Gly561Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475315 n.1658A>G non_coding_transcript_exon_variant 1.0
rpsA 1834509 p.Ile323Thr missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155003 p.Gly370Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290107 c.-866T>A upstream_gene_variant 1.0
kasA 2518576 c.464delG frameshift_variant 0.2
folC 2747360 p.Arg80Leu missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448707 c.204G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642047 c.513G>T synonymous_variant 0.12
fbiB 3642296 c.762G>A synonymous_variant 0.11
fbiB 3642687 c.1154delT frameshift_variant 0.1
alr 3840532 c.888delG frameshift_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242042 p.Met727Thr missense_variant 0.11
embC 4242556 p.Leu898Phe missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243622 c.390G>A synonymous_variant 0.14
embA 4244174 c.942G>A synonymous_variant 0.13
aftB 4267811 c.1026G>A synonymous_variant 0.13
aftB 4269507 c.-671G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408064 p.Arg47Trp missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0