TB-Profiler result

Run: SRR23862009
Summary

Run ID: SRR23862009

Sample name:

Date: 12-04-2023 14:34:26

Number of reads: 3514489

Percentage reads mapped: 99.67

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 gid c.386delG (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
gid 4407816 c.386delG frameshift_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 576093 p.Pro249Arg missense_variant 0.19
mshA 576100 p.Asp251Glu missense_variant 0.17
mshA 576101 p.Arg252Gly missense_variant 0.17
mshA 576116 p.Ala257Pro missense_variant 0.15
mshA 576574 c.1227T>C synonymous_variant 1.0
rpoC 763619 p.Arg84Cys missense_variant 1.0
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475778 n.2121G>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087828 p.Pro337Thr missense_variant 0.18
Rv3083 3448425 c.-78_-74delTCACC upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.15
clpC1 4040235 p.Gly157Ala missense_variant 0.13
clpC1 4040249 p.Glu152Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246542 p.Ser10Thr missense_variant 0.15
embB 4246552 p.Asn13Lys missense_variant 0.15
embB 4246574 p.Ala21Ser missense_variant 0.15
embB 4247013 p.Pro167Arg missense_variant 0.27
embB 4247028 p.Leu172Arg missense_variant 0.21
ethR 4328030 p.Ala161Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0