TB-Profiler result

Run: ERR12544390
Summary

Run ID: ERR12544390

Sample name:

Date: 22-02-2024 18:14:06

Number of reads: 2526341

Percentage reads mapped: 99.65

Strain: lineage4.2.1.1

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 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576488 p.Val381Leu missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777702 p.Thr260Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801201 c.393C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473049 n.1205dupA non_coding_transcript_exon_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.29
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519062 c.948T>G synonymous_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.12
pepQ 2860162 p.Arg86Pro missense_variant 0.13
ribD 2987242 p.Arg135Leu missense_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 0.17
fbiD 3339744 c.627A>C synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.43
rpoA 3878599 c.-92C>G upstream_gene_variant 0.44
rpoA 3878639 c.-132C>G upstream_gene_variant 0.27
embC 4242543 p.Arg894Pro missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.26
embB 4246548 p.Pro12Gln missense_variant 0.28
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.3
embB 4246567 c.54G>T synonymous_variant 0.3
ethR 4327820 p.Ala91Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0