TB-Profiler result

Run: ERR8025696
Summary

Run ID: ERR8025696

Sample name:

Date: 20-05-2023 21:19:09

Number of reads: 3138075

Percentage reads mapped: 99.51

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.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (1.00), pncA c.517dupG (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.-17G>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 0.99
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 761110 p.Asp435Val 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 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, 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 8831 p.Leu510Phe missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619740 c.-151C>T upstream_gene_variant 0.12
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
mmpL5 776252 p.Lys743Asn missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781559 c.-1G>A upstream_gene_variant 1.0
fbiC 1303793 p.Gln288Arg missense_variant 1.0
fbiC 1305054 p.Met708Ile missense_variant 0.13
fbiC 1305086 p.Trp719Leu missense_variant 0.12
Rv1258c 1407093 p.Gly83Asp missense_variant 0.12
Rv1258c 1407192 p.Ala50Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472723 n.878G>T non_coding_transcript_exon_variant 0.15
rrl 1475260 n.1608delG non_coding_transcript_exon_variant 0.1
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
katG 2154945 c.1167C>A synonymous_variant 0.14
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
pepQ 2859624 c.795G>T synonymous_variant 0.12
pepQ 2859774 c.645C>T synonymous_variant 0.12
thyX 3067431 c.514delC frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474013 p.Pro3Ser missense_variant 0.14
Rv3236c 3612098 p.Ile340Thr missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640896 p.Met118Ile missense_variant 0.12
fbiA 3640910 c.373delC frameshift_variant 0.13
rpoA 3878656 c.-149C>A upstream_gene_variant 0.14
clpC1 4040489 p.Gln72His missense_variant 0.14
embC 4239861 c.-2T>C upstream_gene_variant 0.15
embC 4240684 p.Asp274Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244642 c.1410G>T synonymous_variant 0.13
embA 4245290 c.2058C>A synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267775 c.1062T>C synonymous_variant 0.2
ethA 4327022 p.Phe151Tyr missense_variant 0.12
ethA 4327548 c.-75C>A upstream_gene_variant 0.2
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