TB-Profiler result

Run: SRR671740

Summary

Run ID: SRR671740

Sample name:

Date: 20-10-2023 21:45:43

Number of reads: 5353321

Percentage reads mapped: 99.48

Strain: lineage4.4.2

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Tyr (1.00)
Isoniazid R katG p.Val1Ala (0.99)
Ethambutol R embB p.Met306Val (0.99)
Pyrazinamide R pncA c.-219_*13198del (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.99)
Moxifloxacin R gyrA p.Ala90Val (0.99)
Ofloxacin R gyrA p.Ala90Val (0.99)
Levofloxacin R gyrA p.Ala90Val (0.99)
Ciprofloxacin R gyrA p.Ala90Val (0.99)
Aminoglycosides R rrs n.1401A>G (0.99)
Amikacin R rrs n.1401A>G (0.99)
Capreomycin R rrs n.1401A>G (0.99)
Kanamycin R rrs n.1401A>G (0.99)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2156110 p.Val1Ala missense_variant 0.99 isoniazid
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
pncA 2275482 c.-219_*13198del transcript_ablation 1.0 pyrazinamide
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 5731 c.492C>T synonymous_variant 1.0
gyrB 6066 p.Val276Ala missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9107 c.1806C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760939 p.Leu378Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>A upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156052 c.60T>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987312 c.474C>T synonymous_variant 0.98
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448727 p.Leu75Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243991 c.759T>G synonymous_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4248004 p.Gln497His missense_variant 0.99
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0