————Bridging the genotype–phenotype gap to accelerate
mining candidate variation of traits in Brassica napus
Customized phenotype association
(ZS11)
Note that although accession names overlap with those in the database, the seed stocks might be sourced from
different origins with potentially different degrees of purity, or maintained in different collections with
the possibility of outcrossing, which lead to an unreliable result.
Note: no data available, maybe no homologous gene of your input gene id/gene index/region was found or you input a
too long region (>100 kb), please recheck your input format.
Basic Information of gene
Select
ZS11 Gene ID
Darmor Gene ID
AtGI/Name
Position
Seq/Exp/JBR
SNPs No.
SNP No.(High/Moderate/Low/Modifer)
SV No.
SV No.(INS/DEL)
Phylogenetic tree, gene structure and variation
distribution
hovered region:
Define the upstream and downstream of gene
Choose flanking region of gene to show.
Gene structure and SV distribution
The inverted triangle symbols indicate variations, click it to see detailed information in table.
SV information in and its ±
kb flanking region
Select
Chromosome
Start
End
ID
Len
Ref
Alt
JBrowser
Freq
Customize phenotype
select
trait
p-value: (t-test); (wilcox-test)
SV in subpopulation
yes
no
yes
no
Geographical distribution map of
yes
no
Expression of
yes
no
p-value: (t-test); (wilcox-test)
Define the upstream and downstream of gene
Choose flanking regions of gene to show.
Gene structure and SNP distribution
The inverted triangle symbols indicate variations, click it to see detailed information in table.
According to the gene you input, we provide basic snp information. (PIC: polymorphism information
content)
Chromosome
Posistion
Alt (allele)
Ref (allele)
JBrowser
Alt (frequency)
Ref (frequency)
PIC
Alt (num)
Ref (num)
Function_type
Variation_type
Functional_annotations
Information of Haplotypes in and its ± 0 kb flanking region
According
to the gene/region you input,we extract haplotype
information.Note that selected frequency all exceed 0.010.And heterozygous and missing records have been
filtered out.
ID
Haplotype
Frequency
Sample
Customized phenotype
select
trait
p-value:(Anova)
Haplotype
Haplotype
P-value(t-test)
P-value(wilcox-test)
Allele frequency of haplotype in Subpopulation
According to the haplotype you submit, the chart shows the proportion of each sub-population in the
haplotypes. hap_i(n) means the no.i haplotype had n pieces of material.
yes
no
yes
no
Geographic distribution of haplotypes in
According
to the haplotype you submit, the chart shows the proportion of haplotypes in different continents. hap_i(n)
means
the no.i haplotype had n pieces of material.
yes
no
Haplotype
Haplotype
P-value(t-test)
P-value(wilcox-test)
Expression of
Haplotype expression violin in region ± 0 kb
According
to the haplotype you submit, the chart shows the expression level of haplotypes.
yes
no
p-value:(Anova)
Haplotype
Haplotype
P-value(t-test)
P-value(wilcox-test)
Information of SNPs in and its ± 0 kb flanking region
According to the gene you input, we provide basic snp information. (PIC: polymorphism information
content)
BnVIR
Brassica
napus variation information resource
————Bridging the genotype–phenotype gap to accelerate
mining candidate variation of traits in Brassica napus
