TB-Profiler result

Run: ERR4822559
Summary

Run ID: ERR4822559

Sample name:

Date: 20-10-2023 00:54:12

Number of reads: 4402664

Percentage reads mapped: 99.68

Strain: lineage4.8;lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.32
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.7
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.28
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 0.36
gyrA 8040 p.Gly247Ser missense_variant 0.24
gyrA 8806 p.Asp502Ala missense_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 0.21
gyrA 9432 p.Leu711Met missense_variant 0.74
ccsA 620358 c.468C>T synonymous_variant 0.78
rpoB 760115 p.Asp103Glu missense_variant 0.3
rpoC 763025 c.-345C>T upstream_gene_variant 0.68
rpoC 764995 c.1626C>G synonymous_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406607 p.Val245Ala missense_variant 0.68
Rv1258c 1406631 p.Ala237Val missense_variant 0.61
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.63
rpsA 1834836 p.Met432Thr missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102903 p.Thr47Ser missense_variant 0.27
katG 2156196 c.-85C>T upstream_gene_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.33
folC 2746340 p.Ala420Val missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 0.24
ald 3086966 p.Asp49Glu missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.27
whiB7 3568584 c.96C>T synonymous_variant 0.65
ddn 3986944 p.Gly34Glu missense_variant 0.28
clpC1 4038287 c.2418C>T synonymous_variant 0.3
clpC1 4038968 c.1737G>A synonymous_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326184 c.1290C>T synonymous_variant 0.65
whiB6 4338507 c.15C>T synonymous_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.27