TB-Profiler result

Run: ERR779901

Summary

Run ID: ERR779901

Sample name:

Date: 19-10-2023 12:50:45

Number of reads: 5497137

Percentage reads mapped: 99.82

Strain: lineage4.3.4.2

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.Met306Ile (1.00)
Pyrazinamide R pncA c.474_475dupCC (0.14), pncA p.Gly78Cys (0.34)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.15), gyrA p.Asp94His (0.70)
Moxifloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94His (0.70)
Ofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94His (0.70)
Levofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94His (0.70)
Ciprofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94His (0.70)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 7570 p.Ala90Val missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94His missense_variant 0.7 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288766 c.474_475dupCC frameshift_variant 0.14 pyrazinamide
pncA 2289010 p.Gly78Cys missense_variant 0.34 pyrazinamide
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 6140 p.Val301Leu missense_variant 1.0
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 764918 p.Val517Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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
rpsA 1833469 c.-73G>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pncA 2289042 p.Ser67Leu missense_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
ethA 4327064 p.Cys137Tyr missense_variant 1.0
whiB6 4338199 c.322dupG frameshift_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Leu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99