TB-Profiler result

Run: ERR8025523
Summary

Run ID: ERR8025523

Sample name:

Date: 18-05-2023 00:42:30

Number of reads: 2706057

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 katG p.Ser315Thr (1.00)
Ethambutol R embA p.Gly321Ser (0.14), embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Asp8Asn (1.00)
Streptomycin R rpsL p.Lys43Arg (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
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.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289220 p.Asp8Asn missense_variant 1.0 pyrazinamide
embA 4244193 p.Gly321Ser missense_variant 0.14 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 c.1530G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.91
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760074 p.Ile90Phe missense_variant 0.24
rpoB 760761 p.Gly319Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764084 p.Asn239Asp missense_variant 0.1
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
fbiC 1305055 p.Met709Val missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673708 p.Gly90Asp missense_variant 0.11
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 2155336 p.Asp259Val missense_variant 0.12
katG 2155597 p.Ala172Glu missense_variant 0.13
katG 2155695 c.417C>G synonymous_variant 0.15
katG 2155764 c.348C>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987303 c.465G>A synonymous_variant 0.11
ribD 2987325 p.Ile163Phe missense_variant 0.11
Rv2752c 3067125 c.-934C>T upstream_gene_variant 0.13
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339386 c.272dupC frameshift_variant 0.14
Rv3083 3449141 p.Ser213Tyr missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612259 c.858G>A synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841356 p.Ser22Leu missense_variant 1.0
rpoA 3877963 p.Arg182Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244497 p.Ala422Glu missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269216 c.-380C>A upstream_gene_variant 0.12
ethA 4327322 p.Pro51His missense_variant 1.0
whiB6 4338543 c.-22A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407578 p.Lys209Glu missense_variant 0.11
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0