TB-Profiler result

Run: ERR11243548
Summary

Run ID: ERR11243548

Sample name:

Date: 21-04-2023 21:31:37

Number of reads: 754588

Percentage reads mapped: 99.6

Strain: lineage2.2.1

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.Thr394Ala (0.17), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (1.00), embB p.Tyr334His (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Tyr (1.00)
Moxifloxacin R gyrA p.Asp94Tyr (1.00)
Ofloxacin R gyrA p.Asp94Tyr (1.00)
Levofloxacin R gyrA p.Asp94Tyr (1.00)
Ciprofloxacin R gyrA p.Asp94Tyr (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.341delA (0.70), ethA c.341delA (0.70)
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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154932 p.Thr394Ala missense_variant 0.17 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 1.0 ethambutol
ethA 4327132 c.341delA frameshift_variant 0.7 ethionamide, 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
gyrB 6735 p.Asn499Ser missense_variant 0.72
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 575907 p.Ala187Val missense_variant 1.0
ccsA 620265 c.375C>T synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761960 p.Met718Ile missense_variant 0.11
rpoB 762444 p.Ala880Thr missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763058 c.-312C>A upstream_gene_variant 0.1
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800991 c.183G>A synonymous_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406957 c.384G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674812 p.Gly204Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102505 p.Pro180Ser missense_variant 0.13
ndh 2102720 p.Tyr108Cys missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168130 p.Pro828Arg missense_variant 0.1
PPE35 2170353 p.Ala87Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290071 c.-832_-831delTT upstream_gene_variant 0.14
folC 2746718 p.His294Arg missense_variant 0.12
folC 2747406 p.Pro65Ser missense_variant 0.12
pepQ 2859326 p.Phe365Leu missense_variant 0.11
pepQ 2859734 c.684dupG frameshift_variant 0.14
pepQ 2859823 p.Asn199Ser missense_variant 0.11
ribD 2987468 p.Glu210Asp missense_variant 0.1
Rv2752c 3065018 p.Asn392Asp missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641550 p.His6Asn missense_variant 0.11
clpC1 4038739 p.Asp656Asn missense_variant 1.0
embC 4239878 c.20delC frameshift_variant 0.13
embC 4241638 c.1776G>T synonymous_variant 0.22
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 0.95
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