TB-Profiler result

Run: ERR8975789

Summary

Run ID: ERR8975789

Sample name:

Date: 20-10-2023 15:46:17

Number of reads: 7590169

Percentage reads mapped: 99.74

Strain: lineage4.9;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.Asp435Val (0.28), rpoB p.Ser450Leu (0.68)
Isoniazid R fabG1 c.-17G>T (0.26), katG p.Ser315Thr (0.26)
Ethambutol R embB p.Met306Ile (0.21)
Pyrazinamide R pncA c.517dupG (0.27), pncA c.517dupG (0.27)
Streptomycin R rrs n.514A>C (0.27), gid p.Leu79Ser (0.23)
Fluoroquinolones R gyrA p.Asp94Asn (0.25)
Moxifloxacin R gyrA p.Asp94Asn (0.25)
Ofloxacin R gyrA p.Asp94Asn (0.25)
Levofloxacin R gyrA p.Asp94Asn (0.25)
Ciprofloxacin R gyrA p.Asp94Asn (0.25)
Aminoglycosides R rrs n.1401A>G (0.27)
Amikacin R rrs n.1401A>G (0.27)
Capreomycin R rrs n.1401A>G (0.27)
Kanamycin R rrs n.1401A>G (0.27)
Cycloserine R alr p.Leu113Arg (0.27)
Ethionamide R fabG1 c.-17G>T (0.26), ethA p.Ala381Pro (0.31)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.27)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.27
lineage4 Euro-American LAM;T;S;X;H None 0.73
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.26
lineage4.9 Euro-American (H37Rv-like) T1 None 0.75
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.27
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 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.28 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.27 linezolid
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.27 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.26 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.26 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.27 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 0.27 cycloserine
embB 4247431 p.Met306Ile missense_variant 0.21 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.31 ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.23 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 0.25
gyrA 9304 p.Gly668Asp missense_variant 0.29
gyrA 9311 c.2010C>T synonymous_variant 0.7
fgd1 491742 c.960T>C synonymous_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 0.28
mmpL5 776100 p.Thr794Ile missense_variant 0.31
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.26
Rv1979c 2221939 p.Arg409Gln missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 0.24
embA 4243460 c.228C>T synonymous_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.25
ethR 4327042 c.-507G>A upstream_gene_variant 0.75
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.26
gid 4407927 p.Glu92Asp missense_variant 0.26