TB-Profiler result

Run: SRR23861985
Summary

Run ID: SRR23861985

Sample name:

Date: 12-04-2023 13:23:37

Number of reads: 4626417

Percentage reads mapped: 99.5

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 0.89
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.89
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.87
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 0.89
gyrA 9304 p.Gly668Asp missense_variant 0.89
mshA 576077 p.Leu244Val missense_variant 0.14
mshA 576093 p.Pro249Arg missense_variant 0.21
mshA 576119 p.Ala258Pro missense_variant 0.13
ccsA 620059 p.Asp57His missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471647 n.-199G>A upstream_gene_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475919 n.2262C>A non_coding_transcript_exon_variant 0.84
inhA 1673970 c.-232C>A upstream_gene_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 0.85
fbiD 3339739 p.Ala208Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.93
whiB7 3568416 p.Lys88His missense_variant 0.13
whiB7 3568428 c.252A>C synonymous_variant 0.18
clpC1 4040235 p.Gly157Ala missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246574 p.Ala21Ser missense_variant 0.13
embB 4247013 p.Pro167Arg missense_variant 0.15
embB 4247016 p.Ser168Trp missense_variant 0.15
ethR 4328030 p.Ala161Gly missense_variant 0.16
ethR 4328045 p.Leu166Gln missense_variant 0.17
ethR 4328060 p.Leu171Gln missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.91