TB-Profiler result

Run: ERR8025441

Summary

Run ID: ERR8025441

Sample name:

Date: 19-05-2023 15:55:38

Number of reads: 5733056

Percentage reads mapped: 99.57

Strain: lineage2.2.2

Drug-resistance: XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Asp (0.99)
Isoniazid R fabG1 c.-15C>T (0.99)
Ethambutol
Pyrazinamide R pncA p.Thr142Met (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Asn (0.99)
Moxifloxacin R gyrA p.Asp94Asn (0.99)
Ofloxacin R gyrA p.Asp94Asn (0.99)
Levofloxacin R gyrA p.Asp94Asn (0.99)
Ciprofloxacin R gyrA p.Asp94Asn (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>A (0.99)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.99), ethA p.Ala381Pro (1.00)
Clofazimine R mmpR5 c.198dupG (0.29)
Para-aminosalicylic_acid
Delamanid
Bedaquiline R mmpR5 c.198dupG (0.29)
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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 7581 p.Asp94Asn missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 0.99 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.29 clofazimine, bedaquiline
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.99 kanamycin
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
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 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779263 c.275dupA frameshift_variant&stop_gained 0.19
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0