TB-Profiler result

Run: ERR8975724
Summary

Run ID: ERR8975724

Sample name:

Date: 20-10-2023 15:39:32

Number of reads: 4866521

Percentage reads mapped: 99.74

Strain: lineage4.4.1.1.1

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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Val139Ala (1.00)
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.436_437dupGC (0.20), ald c.897_898dupGA (0.57)
Ethionamide R ethA c.777dupC (0.34)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans None 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.2 cycloserine
ald 3087715 c.897_898dupGA frameshift_variant 0.57 cycloserine
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326696 c.777dupC frameshift_variant 0.34 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759960 p.Thr52Pro missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859601 c.817dupG frameshift_variant 0.37
pepQ 2860268 c.150dupC frameshift_variant 0.58
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086863 p.Arg15Gln missense_variant 0.11
ald 3087842 c.1025dupG frameshift_variant 0.14
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269721 p.Ala38Val missense_variant 1.0
ethA 4326126 p.Gly450Ser missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0