TB-Profiler result

Run: ERR4822354
Summary

Run ID: ERR4822354

Sample name:

Date: 20-10-2023 01:31:10

Number of reads: 3223885

Percentage reads mapped: 99.44

Strain: lineage4.2.2

Drug-resistance: MDR-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.Leu430Pro (1.00), rpoB p.Asp435Tyr (1.00), rpoB p.Ser441Ala (1.00)
Isoniazid R ahpC c.-52C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.86
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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 1.0 rifampicin
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
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 7121 p.Pro628Ala 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
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576224 p.Val293Trp missense_variant 0.98
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
katG 2155928 p.Phe62Leu missense_variant 1.0
Rv1979c 2222537 p.Val210Phe missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064646 p.Glu516* stop_gained 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
thyA 3074042 p.Pro144Ser missense_variant 1.0
thyA 3074095 c.376delC frameshift_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087488 c.669C>T synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568819 c.-140C>G upstream_gene_variant 1.0
clpC1 4040110 p.Arg199Gly missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244400 p.Leu390Met missense_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4248027 p.Ala505Val missense_variant 1.0
embB 4249533 p.Ala1007Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407988 p.Ala72Asp missense_variant 0.99