TB-Profiler result

Run: SRR671862

Summary

Run ID: SRR671862

Sample name:

Date: 20-10-2023 21:50:38

Number of reads: 6117594

Percentage reads mapped: 99.48

Strain: lineage4.4.2

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.Ser315Asn (0.98)
Ethambutol R embA c.-11C>A (0.98)
Pyrazinamide R pncA c.282_*290del (0.99)
Streptomycin R gid p.Lys163* (0.99)
Fluoroquinolones R gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84)
Moxifloxacin R gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84)
Ofloxacin R gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84)
Levofloxacin R gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84)
Ciprofloxacin R gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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 7566 p.Asp89Asn missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.84 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Asn missense_variant 0.98 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 0.98 ethambutol
gid 4407716 p.Lys163* stop_gained 0.99 streptomycin
pncA 2288390 c.282_*290del frameshift_variant&stop_lost&splice_region_variant 0.99 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575503 c.156G>A synonymous_variant 0.99
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 2102365 c.678A>C synonymous_variant 0.97
katG 2156484 c.-373A>G upstream_gene_variant 1.0
PPE35 2169411 c.1201dupA frameshift_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244329 p.Ala366Glu missense_variant 0.99
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4248026 p.Ala505Thr missense_variant 0.73
aftB 4267512 p.Leu442His missense_variant 0.98
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 0.97
ethA 4326977 p.His166Pro missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0