TB-Profiler result

Run: SRR23862155

Summary

Run ID: SRR23862155

Sample name:

Date: 12-04-2023 21:13:14

Number of reads: 5086147

Percentage reads mapped: 99.65

Strain: lineage4.8

Drug-resistance: Other


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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 R rpsL p.Lys43Arg (1.00)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
mshA 576108 p.Ala254Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.15
pepQ 2860159 p.Ala87Gly missense_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.78
fbiD 3339751 p.Ala212Pro missense_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.33
whiB7 3568431 c.249C>G synonymous_variant 0.29
rpoA 3878609 c.-102T>C upstream_gene_variant 0.25
rpoA 3878613 c.-106A>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.52
embC 4240409 p.Pro183Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328378 c.-905G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0