TB-Profiler result

Run: ERR11083031
Summary

Run ID: ERR11083031

Sample name:

Date: 11-04-2023 17:43:35

Number of reads: 2845406

Percentage reads mapped: 99.48

Strain: lineage4.2.2.2

Drug-resistance: Other

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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 R gyrA p.Ala90Val (0.28)
Moxifloxacin R gyrA p.Ala90Val (0.28)
Ofloxacin R gyrA p.Ala90Val (0.28)
Levofloxacin R gyrA p.Ala90Val (0.28)
Ciprofloxacin R gyrA p.Ala90Val (0.28)
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
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
gyrA 7570 p.Ala90Val missense_variant 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 7581 p.Asp94Ser missense_variant 0.45
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576453 p.Val369Gly missense_variant 0.19
mshA 576456 p.Val370Gly missense_variant 0.27
mshA 576615 p.Arg423Pro missense_variant 0.14
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101764 p.Gly427Ser missense_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.34
pepQ 2860159 p.Ala87Gly missense_variant 0.18
Rv2752c 3064823 p.Val457Leu missense_variant 0.23
Rv2752c 3066280 c.-89C>T 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
ald 3087816 p.Cys333Gly missense_variant 0.14
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fbiD 3339751 p.Ala212Pro missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.15
whiB7 3568428 c.252A>C synonymous_variant 0.29
rpoA 3878590 c.-83G>C upstream_gene_variant 0.75
rpoA 3878641 c.-134C>G upstream_gene_variant 0.83
embC 4240409 p.Pro183Ala missense_variant 0.55
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244091 p.Ala287Thr missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.48
embB 4248328 c.1815G>C synonymous_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0