TB-Profiler result

Run: SRR25827542

Summary

Run ID: SRR25827542

Sample name:

Date: 02-02-2024 09:28:25

Number of reads: 4956895

Percentage reads mapped: 99.4

Strain: lineage4.4.1.2

Drug-resistance: 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 (0.97)
Ethambutol R embB p.Gln497Arg (0.99)
Pyrazinamide R pncA c.496dupG (0.99)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrA p.Asp94Ala (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R ethA c.1370_1371dupTG (0.98)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.99)
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 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.2 Euro-American T1 None 0.99
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.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.99 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2288745 c.496dupG frameshift_variant 0.99 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol
ethA 4326102 c.1370_1371dupTG frameshift_variant 0.98 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
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779130 c.144dupC frameshift_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406451 p.Thr297Ile missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.98
PPE35 2167770 p.Ser948Ile missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747479 p.Glu40Asp missense_variant 0.54
pepQ 2860213 p.Pro69Leu missense_variant 0.98
thyA 3073723 p.Asn250Ser missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642528 p.Glu332Lys missense_variant 0.99
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4249012 c.2499G>A synonymous_variant 0.98
aftB 4267939 p.Arg300Trp missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408186 p.Pro6Arg missense_variant 1.0