TB-Profiler result

Run: ERR8025605
Summary

Run ID: ERR8025605

Sample name:

Date: 23-05-2023 04:55:03

Number of reads: 2436976

Percentage reads mapped: 99.54

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)
Ethambutol R embB p.Asp354Ala (1.00)
Pyrazinamide R pncA p.Tyr103* (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 R fabG1 c.-15C>T (1.00), 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.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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
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 5602 c.363C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765992 c.2623C>A synonymous_variant 0.13
rpoC 766957 p.Glu1196Asp missense_variant 0.15
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
mmpR5 779254 c.267delG frameshift_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.95
fbiC 1303236 c.306C>T synonymous_variant 0.12
fbiC 1303313 p.Ile128Asn missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407465 c.-125G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472624 n.779T>A non_coding_transcript_exon_variant 0.12
rrs 1473057 n.1212G>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918734 c.795C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156297 c.-186T>C upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714905 p.Asp143Gly missense_variant 0.13
folC 2746861 c.738G>A synonymous_variant 0.12
folC 2747303 p.Pro99Leu missense_variant 0.12
folC 2747318 p.Gly94Asp missense_variant 0.12
pepQ 2859645 c.774G>A synonymous_variant 0.17
pepQ 2860221 c.198G>A synonymous_variant 0.17
ribD 2986728 c.-111C>A upstream_gene_variant 0.12
Rv2752c 3064729 p.Ala488Val missense_variant 0.17
thyA 3074610 c.-139G>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339303 c.188_198delCCCCCGACGAA frameshift_variant 0.12
fbiD 3339706 p.Ala197Thr missense_variant 0.14
Rv3083 3449968 p.Ala489Thr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475366 p.Gly454Arg missense_variant 0.25
whiB7 3568443 c.237C>T synonymous_variant 0.14
Rv3236c 3612010 c.1107G>T synonymous_variant 0.12
Rv3236c 3612041 p.Val359Ala missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640999 p.His153Asn missense_variant 0.13
fbiB 3642075 p.Asp181Asn missense_variant 0.14
fbiB 3642156 p.Lys208Glu missense_variant 0.15
fbiB 3642316 p.Arg261Met missense_variant 0.25
rpoA 3878035 p.Glu158Gly missense_variant 0.1
clpC1 4038428 c.2277G>A synonymous_variant 0.13
embC 4242614 p.Ala918Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242700 c.-533C>T upstream_gene_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243704 p.Gly158Arg missense_variant 0.13
embA 4246485 p.Gly1085Ser missense_variant 0.11
embB 4247415 p.Gly301Asp missense_variant 0.11
embB 4248404 p.Ala631Ser missense_variant 0.11
embB 4249562 p.Asp1017Tyr missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267693 c.1143dupG frameshift_variant 0.12
aftB 4267833 p.His335Arg missense_variant 0.22
ubiA 4269317 p.Ser173Ala missense_variant 1.0
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