TB-Profiler result

Run: ERR11465125
Summary

Run ID: ERR11465125

Sample name:

Date: 09-01-2024 18:43:42

Number of reads: 7370003

Percentage reads mapped: 99.68

Strain: lineage4.7;lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.46
lineage4.7 Euro-American (mainly T) T1;T5 None 0.52
lineage4.3.4 Euro-American (LAM) LAM RD174 0.46
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.41
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 0.39
gyrA 9304 p.Gly668Asp missense_variant 0.45
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoC 764995 c.1626C>G synonymous_variant 0.41
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 1474294 n.637C>G non_coding_transcript_exon_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101789 c.1254G>A synonymous_variant 0.5
Rv1979c 2222854 p.Ile104Thr missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.43
whiB7 3568610 p.Asp24His missense_variant 0.53
Rv3236c 3612009 p.Ala370Thr missense_variant 0.53
alr 3840618 p.Asp268Gly missense_variant 0.54
clpC1 4038287 c.2418C>T synonymous_variant 0.54
clpC1 4039991 c.714G>A synonymous_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243929 p.Leu233Met missense_variant 0.55
embB 4249732 c.3219C>G synonymous_variant 0.6
ethA 4328235 c.-762C>T upstream_gene_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.47