TB-Profiler result

Run: SRR2100721

Summary

Run ID: SRR2100721

Sample name:

Date: 19-10-2023 16:27:20

Number of reads: 2836028

Percentage reads mapped: 99.5

Strain: lineage4.1.1.3.1

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.Ile491Phe (0.88)
Isoniazid
Ethambutol R embB p.Met306Ile (0.92)
Pyrazinamide R pncA p.Lys96Glu (0.16), pncA p.Val7Leu (0.60), pncA c.-5delG (0.25)
Streptomycin R gid c.102delG (0.96)
Fluoroquinolones R gyrA p.Asp94Gly (0.95)
Moxifloxacin R gyrA p.Asp94Gly (0.95)
Ofloxacin R gyrA p.Asp94Gly (0.95)
Levofloxacin R gyrA p.Asp94Gly (0.95)
Ciprofloxacin R gyrA p.Asp94Gly (0.95)
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 0.95
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.93
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.94
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 0.93
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 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 0.88 rifampicin
pncA 2288956 p.Lys96Glu missense_variant 0.16 pyrazinamide
pncA 2289223 p.Val7Leu missense_variant 0.6 pyrazinamide
pncA 2289245 c.-5delG upstream_gene_variant 0.25 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.92 ethambutol
gid 4408100 c.102delG frameshift_variant 0.96 streptomycin
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 0.98
rpoC 765150 p.Gly594Glu missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154695 p.Val473Leu missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.95
embB 4249408 c.2895G>A synonymous_variant 0.97
aftB 4269540 c.-704C>T upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0