TB-Profiler result

Run: SRR23861894
Summary

Run ID: SRR23861894

Sample name:

Date: 12-04-2023 09:02:59

Number of reads: 5369939

Percentage reads mapped: 99.48

Strain: lineage4.2.1.1

Drug-resistance: RR-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.Ser450Ala (0.13)
Isoniazid
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
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
rpoB 761154 p.Ser450Ala missense_variant 0.13 rifampicin
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 576093 p.Pro249Arg missense_variant 0.16
mshA 576113 p.Arg256Gly missense_variant 0.19
mshA 576590 p.Arg415Gly missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 779100 c.-620A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460876 c.-169G>A upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673401 c.-801G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067157 c.-966G>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246542 p.Ser10Thr missense_variant 0.17
embB 4246552 p.Asn13Lys missense_variant 0.19
embB 4246574 p.Ala21Ser missense_variant 0.16
embB 4246999 c.486C>G synonymous_variant 0.15
embB 4247013 p.Pro167Arg missense_variant 0.2
embB 4247016 p.Ser168Trp missense_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-115delC upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0