TB-Profiler result

Run: ERR4799448

Summary

Run ID: ERR4799448

Sample name:

Date: 20-10-2023 03:52:53

Number of reads: 6666913

Percentage reads mapped: 99.61

Strain: lineage2.2.1

Drug-resistance: 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), rpoC p.Ile491Thr (0.98)
Isoniazid R fabG1 c.-8T>A (0.98), katG p.Ser315Thr (0.99)
Ethambutol R embA c.-16C>T (0.99)
Pyrazinamide R pncA p.Ile5Ser (0.97)
Streptomycin R rpsL p.Lys43Arg (0.98)
Fluoroquinolones R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (0.97)
Moxifloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (0.97)
Ofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (0.97)
Levofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (0.97)
Ciprofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (0.97)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine R alr p.Met343Thr (0.99)
Ethionamide
Clofazimine R mmpR5 c.198dupG (0.99)
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.98)
Delamanid
Bedaquiline R mmpR5 c.198dupG (0.99)
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.98 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.99 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.98 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.97 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.98 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 0.99 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 0.99 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_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 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
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
thyX 3067949 c.-4C>T upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
embC 4241022 p.Ala387Val missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4247847 p.Gln445Arg missense_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 0.96
ethA 4327344 p.Thr44Pro missense_variant 0.99
whiB6 4338292 p.Ala77Val missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0