TB-Profiler result

Run: ERR12544386
Summary

Run ID: ERR12544386

Sample name:

Date: 23-02-2024 02:42:29

Number of reads: 4272713

Percentage reads mapped: 99.58

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576488 p.Val381Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.14
fbiC 1303155 c.225G>A synonymous_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.51
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170066 p.Ala183Thr missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.15
fbiD 3339744 c.627A>C synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
rpoA 3878567 c.-60C>G upstream_gene_variant 0.43
rpoA 3878578 c.-71C>A upstream_gene_variant 0.25
rpoA 3878599 c.-92C>G upstream_gene_variant 0.3
rpoA 3878639 c.-132C>G upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.34
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4249594 c.3081G>A synonymous_variant 0.99
ethA 4328376 c.-903G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0