TB-Profiler result

Run: SRR23861728
Summary

Run ID: SRR23861728

Sample name:

Date: 12-04-2023 01:26:35

Number of reads: 4989223

Percentage reads mapped: 99.75

Strain: lineage4.4.1.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576093 p.Pro249Arg missense_variant 0.17
mshA 576100 p.Asp251Glu missense_variant 0.2
mshA 576456 p.Val370Gly missense_variant 0.17
mshA 576468 p.Val374Gly missense_variant 0.16
mshA 576613 c.1266A>C synonymous_variant 0.17
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 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860480 c.-62G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339746 p.Ala210Gly missense_variant 0.23
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.23
whiB7 3568437 c.243T>C synonymous_variant 0.2
whiB7 3568441 p.Lys80Thr missense_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641953 p.Leu140Arg missense_variant 1.0
rpoA 3878600 c.-93G>C upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247007 p.Lys165Thr missense_variant 0.15
embB 4247013 p.Pro167Arg missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0