TB-Profiler result

Run: ERR11082855

Summary

Run ID: ERR11082855

Sample name:

Date: 11-04-2023 09:07:39

Number of reads: 3367591

Percentage reads mapped: 99.47

Strain: lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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
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 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 0.14
mshA 576116 p.Ala257Pro missense_variant 0.18
rpoB 761482 p.Ala559Gly missense_variant 0.2
rpoC 764367 p.Gly333Ala missense_variant 0.17
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
Rv1258c 1406205 p.Thr379Lys missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.14
Rv2752c 3064823 p.Val457Leu missense_variant 0.19
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
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339751 p.Ala212Pro missense_variant 0.31
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.76
clpC1 4040254 p.Ala151Thr missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.24
embC 4240413 p.Leu184Arg missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.47
embB 4246584 p.Arg24Pro missense_variant 0.23
embB 4247016 p.Ser168Trp missense_variant 0.22
embB 4248328 c.1815G>C synonymous_variant 0.16
aftB 4267400 c.1437G>C synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
embR 1412403 c.372_*3777del frameshift_variant&stop_lost&splice_region_variant 1.0