TB-Profiler result

Run: ERR8025695
Summary

Run ID: ERR8025695

Sample name:

Date: 20-05-2023 21:13:40

Number of reads: 2513527

Percentage reads mapped: 99.6

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 c.2156delA (0.12), katG c.2052delT (0.12), 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.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (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.Asp94Gly 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 2153955 c.2156delA frameshift_variant 0.12 isoniazid
katG 2154059 c.2052delT frameshift_variant 0.12 isoniazid
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 9151 p.Tyr617Cys missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575988 p.Ile214Asn missense_variant 0.15
mshA 576164 p.Arg273Cys missense_variant 0.12
mshA 576349 c.1002G>T synonymous_variant 0.14
ccsA 619735 c.-156G>T upstream_gene_variant 0.11
rpoB 760837 p.Glu344Val missense_variant 0.13
rpoB 762760 p.Cys985Tyr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765969 p.Thr867Ile missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779347 p.Val120Met missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801392 c.587delG frameshift_variant 0.12
fbiC 1303495 p.Pro189Ser missense_variant 0.11
embR 1416254 c.1093delG frameshift_variant 0.15
embR 1416303 p.Gly349Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674874 p.Arg225Cys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834953 p.Ala471Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155706 p.Pro136Thr missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168123 c.2490A>G synonymous_variant 0.15
PPE35 2168194 p.Gly807Ser missense_variant 0.14
PPE35 2170578 p.Ser12* stop_gained 0.11
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518720 c.606C>T synonymous_variant 0.14
kasA 2519006 p.Ala298Thr missense_variant 0.13
pepQ 2860361 p.Asp20Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 c.555C>T synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474237 c.231C>G synonymous_variant 0.14
fprA 3474406 c.403_404delCA frameshift_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640689 c.-846C>T upstream_gene_variant 0.11
alr 3840690 p.Pro244His missense_variant 0.11
embC 4241973 p.Val704Ala missense_variant 0.13
embC 4241976 p.Gln705Arg missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246806 p.Val98Ala missense_variant 0.15
embB 4249520 p.Ala1003Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268008 p.Gly277* stop_gained 0.11
aftB 4268316 p.Ala174Glu missense_variant 0.11
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ethA 4328313 c.-840C>A upstream_gene_variant 0.11
ethA 4328367 c.-894C>T upstream_gene_variant 0.13
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