TB-Profiler result

Run: ERR221539

Summary

Run ID: ERR221539

Sample name:

Date: 20-10-2023 22:59:37

Number of reads: 3478200

Percentage reads mapped: 96.88

Strain: lineage4.3.4.2.1;lineage3.1;lineage2.2.1

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
lineage3 East-African-Indian CAS RD750 0.82
lineage2 East-Asian Beijing RD105 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.1
lineage4.3 Euro-American (LAM) mainly-LAM None 0.06
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.07
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.67
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
lineage4.3.4 Euro-American (LAM) LAM RD174 0.07
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.1
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
fgd1 491742 c.960T>C synonymous_variant 0.96
ccsA 620625 p.Ile245Met missense_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 0.89
rpoC 762434 c.-936T>G upstream_gene_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 764995 c.1626C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.9
mmpL5 776182 p.Asp767Asn missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.87
katG 2155334 p.Val260Ile missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.8
pncA 2289365 c.-125delC upstream_gene_variant 0.88
eis 2714926 p.Thr136Ser missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12
embC 4241562 p.Arg567His missense_variant 0.73
embC 4242075 p.Arg738Gln missense_variant 0.63
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.16
embB 4249354 c.2841G>C synonymous_variant 0.73
whiB6 4338592 c.-71G>C upstream_gene_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338706 c.-185C>T upstream_gene_variant 0.79
gid 4407588 c.615A>G synonymous_variant 0.93