TB-Profiler result

Run: ERR8025424

Summary

Run ID: ERR8025424

Sample name:

Date: 19-05-2023 15:27:34

Number of reads: 2657997

Percentage reads mapped: 99.59

Strain: lineage2.2.2

Drug-resistance: Pre-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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Cys14Arg (1.00)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrA p.Asp94Ala (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA p.Ala381Pro (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
mshA 576387 p.Ala347Val missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763947 p.Ala193Gly missense_variant 0.14
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 764879 p.Leu504Met missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
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
pncA 2289818 c.-577T>C upstream_gene_variant 0.1
pncA 2289968 c.-727G>T upstream_gene_variant 0.15
kasA 2518341 p.Asp76Val missense_variant 0.11
folC 2747106 p.Asp165Tyr missense_variant 0.2
pepQ 2859441 c.978C>A synonymous_variant 0.12
Rv2752c 3066994 c.-803A>G upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087095 c.277delA frameshift_variant 0.11
Rv3083 3449145 c.642G>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474347 c.345delC frameshift_variant 0.12
Rv3236c 3612797 p.Ala107Gly missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
panD 4044462 c.-181T>C upstream_gene_variant 0.12
embC 4239664 c.-199C>A upstream_gene_variant 0.11
embC 4239717 c.-146C>A upstream_gene_variant 0.1
embC 4239796 c.-67C>A upstream_gene_variant 0.12
embC 4241060 p.Pro400Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243573 p.Val114Ala missense_variant 0.1
embA 4244611 p.Ala460Val missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267787 c.1050G>T synonymous_variant 0.12
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ubiA 4269957 c.-124A>G upstream_gene_variant 0.12
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