TB-Profiler result

Run: ERR8025743

Summary

Run ID: ERR8025743

Sample name:

Date: 18-05-2023 07:38:13

Number of reads: 2627138

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), inhA p.Ile194Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin
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), inhA p.Ile194Thr (1.00), ethA c.1200_1201dupGT (0.13), ethR p.Ala95Thr (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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 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
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326272 c.1200_1201dupGT frameshift_variant 0.13 ethionamide
ethR 4327831 p.Ala95Thr 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
gyrB 5089 c.-150delG upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7607 c.306C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490986 c.204G>T synonymous_variant 0.11
fgd1 491200 p.Arg140Trp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576040 c.695delC frameshift_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762960 p.Gly1052Cys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 763798 p.Met143Ile missense_variant 0.13
rpoC 763803 p.His145Arg missense_variant 0.12
rpoC 766467 p.Glu1033Val 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 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417519 c.-172C>A upstream_gene_variant 0.13
atpE 1460914 c.-131G>A upstream_gene_variant 0.13
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
ndh 2102041 p.Gln334His missense_variant 0.18
ndh 2102053 c.990G>T synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167754 c.2859C>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223086 p.Ile27Val missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289873 c.-632C>T upstream_gene_variant 0.11
folC 2746194 p.Thr469Ser missense_variant 0.2
folC 2746620 p.Arg327Trp missense_variant 0.11
folC 2747360 p.Arg80His missense_variant 0.14
thyX 3067288 p.Ala220Ser missense_variant 0.12
ald 3086742 c.-78A>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086808 c.-12A>G upstream_gene_variant 0.12
Rv3083 3449157 p.Phe218Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474381 c.375C>T synonymous_variant 0.14
whiB7 3568481 p.Gly67Ser missense_variant 0.14
Rv3236c 3612395 p.Ala241Asp missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612854 p.His88Arg missense_variant 0.13
fbiB 3641540 c.6C>A synonymous_variant 0.14
fbiB 3641570 c.36C>A synonymous_variant 0.13
fbiB 3642155 c.621C>A synonymous_variant 0.15
clpC1 4040331 c.373delG frameshift_variant 0.13
embC 4240601 p.Ala247Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242841 c.-392C>T upstream_gene_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327271 p.Pro68His missense_variant 0.12
whiB6 4338536 c.-15G>T upstream_gene_variant 0.11
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