TB-Profiler result

Run: SRR23861888
Summary

Run ID: SRR23861888

Sample name:

Date: 12-04-2023 08:47:02

Number of reads: 4927047

Percentage reads mapped: 99.87

Strain: lineage4.8

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
lineage4.8 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
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 576456 p.Val370Gly missense_variant 0.23
mshA 576613 c.1266A>C synonymous_variant 0.18
mshA 576615 p.Arg423Pro missense_variant 0.2
mshA 576618 p.His424Pro missense_variant 0.16
mshA 576620 p.Ala425Pro missense_variant 0.26
mshA 576626 p.Thr427Pro missense_variant 0.24
mshA 576651 p.Asp435Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303106 p.Cys59Tyr missense_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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170073 c.540C>G synonymous_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339729 c.612G>C synonymous_variant 0.15
fbiD 3339736 p.Thr207Pro missense_variant 0.18
fbiD 3339744 c.627A>T synonymous_variant 0.38
whiB7 3568425 c.255T>G synonymous_variant 0.16
rpoA 3878590 c.-84C>G upstream_gene_variant 0.22
rpoA 3878609 c.-102T>C upstream_gene_variant 0.18
rpoA 3878613 c.-106A>C upstream_gene_variant 0.2
rpoA 3878614 c.-107A>C upstream_gene_variant 0.14
rpoA 3878618 c.-111A>C upstream_gene_variant 0.18
rpoA 3878619 c.-113delC upstream_gene_variant 0.91
rpoA 3878653 c.-146A>C upstream_gene_variant 0.17
embC 4240427 p.Ser189Cys missense_variant 0.22
embA 4242643 c.-590C>T 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