TB-Profiler result

Run: ERR11243541

Summary

Run ID: ERR11243541

Sample name:

Date: 21-04-2023 21:23:08

Number of reads: 451969

Percentage reads mapped: 99.63

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), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr142Met (1.00)
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.82)
Moxifloxacin R gyrA p.Ala90Val (0.82)
Ofloxacin R gyrA p.Ala90Val (0.82)
Levofloxacin R gyrA p.Ala90Val (0.82)
Ciprofloxacin R gyrA p.Ala90Val (0.82)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.470delT (0.18)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (1.00)
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
lineage2.2.1 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 7570 p.Ala90Val missense_variant 0.82 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327003 c.470delT frameshift_variant 0.18 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
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 764363 p.Gly332Cys missense_variant 1.0
rpoC 766482 p.Arg1038Gln missense_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778464 p.Thr6Ile missense_variant 0.13
mmpS5 778490 p.Val139Ala missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406106 p.Asp412Gly missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461190 p.Leu49Pro missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674108 c.-94C>T upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918166 p.Ala76Val missense_variant 0.13
katG 2154482 p.Val544Ile missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222440 p.Ala242Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714295 c.1038A>T synonymous_variant 0.12
eis 2715455 c.-123G>A upstream_gene_variant 0.18
pepQ 2860184 c.229_234delCGCGCG conservative_inframe_deletion 0.14
pepQ 2860200 c.219G>A synonymous_variant 0.13
pepQ 2860201 c.216_217delAG frameshift_variant 0.13
pepQ 2860207 c.211_212insGCGCGC conservative_inframe_insertion 0.12
thyA 3073714 p.Pro253Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339654 c.537A>G synonymous_variant 0.14
Rv3083 3449638 c.1139delA frameshift_variant 0.12
fprA 3473877 c.-130G>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474069 c.63C>T synonymous_variant 0.14
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641124 p.Ser194Arg missense_variant 0.17
fbiB 3642548 c.1014C>A synonymous_variant 0.18
fbiB 3642731 c.1197C>T synonymous_variant 0.22
rpoA 3877562 c.945delC frameshift_variant 0.13
ddn 3986739 c.-104delG upstream_gene_variant 0.29
clpC1 4040499 p.Gln69Arg missense_variant 0.18
embC 4240857 p.Ala332Val missense_variant 0.29
embC 4241242 c.1380G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246657 c.144C>T synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326705 p.Pro257Ser missense_variant 0.91
ethR 4327867 p.Ile107Leu missense_variant 0.18
ethR 4328168 p.Trp207Leu missense_variant 0.13
whiB6 4338231 c.291C>A synonymous_variant 0.11
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