TB-Profiler result

Run: ERR11243542
Summary

Run ID: ERR11243542

Sample name:

Date: 21-04-2023 21:23:42

Number of reads: 484173

Percentage reads mapped: 99.64

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 (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 1.0 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
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 8104 p.Ser268* stop_gained 0.15
gyrA 8776 p.Asp492Val missense_variant 0.17
gyrA 9275 p.Glu658Asp missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9601 p.Ile767Asn missense_variant 0.14
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
rpoB 760893 p.Asp363Tyr missense_variant 0.11
rpoB 762003 p.Asn733Asp missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767145 p.Pro1259Gln missense_variant 0.14
rpoC 767202 p.Ala1278Asp missense_variant 0.17
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 776454 p.Met676Thr missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303107 c.177C>T synonymous_variant 0.14
fbiC 1303855 p.Ala309Ser missense_variant 0.15
fbiC 1303858 p.Gly310* stop_gained 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471772 n.-74G>A upstream_gene_variant 0.29
fabG1 1673609 p.Gly57Asp missense_variant 0.29
rpsA 1833704 p.Ile55Phe missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834644 p.Asp368Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102419 p.Lys208Asn missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073714 p.Pro253Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087488 c.669C>T synonymous_variant 0.2
fbiD 3339640 p.Ala175Thr missense_variant 0.12
fprA 3473836 c.-171C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>T synonymous_variant 0.13
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640993 p.Glu151Lys missense_variant 0.12
fbiB 3641748 p.Arg72* stop_gained 0.14
alr 3840385 p.Phe346Leu missense_variant 0.14
alr 3840822 p.Ala200Asp missense_variant 0.11
rpoA 3877545 c.963G>A synonymous_variant 0.11
rpoA 3877618 p.Val297Glu missense_variant 0.14
clpC1 4039124 c.1581C>T synonymous_variant 0.17
clpC1 4039500 p.Leu402Pro missense_variant 0.4
panD 4043874 c.408C>A synonymous_variant 0.11
embC 4240673 p.Gly271Ser missense_variant 0.17
embC 4241177 p.Gly439Arg missense_variant 0.25
embC 4242050 p.Gln730Lys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245290 c.2058C>G synonymous_variant 0.11
embA 4245660 p.Ala810Ser missense_variant 0.29
embA 4246024 p.Trp931Leu missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268257 p.Gly194Arg missense_variant 0.12
ubiA 4269747 c.86delA frameshift_variant 0.12
ethA 4326705 p.Pro257Ser 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