Single-locus model
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Basic information of gene(s)
| Gene ID | AtGI/Name | Position | Seq/Exp/JBR | SNPs No. | SNP No.(High/Moderate/Low/Modifier) | SV No. | SV No.(INS/DEL) | Multi-locus selector |
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Phylogenetic tree, gene structure and variation distribution
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.
| Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
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Annotation and statistics of SNPs
Information of SNPs in and its ± kb flanking region
PIC: polymorphism information content
| Selector | Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
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Information of SNPs in and its ± kb flanking region
PIC: polymorphism information content
| Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
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Information of Haplotypes in and its ± 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 |
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SV information in and its ± kb flanking region
| Selector | Chr. | Start | End | ID | Len | Ref | Alt | Freq | JBrowser |
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Allele frequency of different Subpopulation
Geographical distribution plot
Violin plot of phenotypic value
p-value: (t-test); (wilcoxon-test)
| Selector | Chr. | Position | Alt (allele) | Ref (allele) | JBrowser | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
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| ID | Haplotype | Frequency | Sample |
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| Selector | Chr. | Start | End | ID | Len | Ref | Alt | Freq | JBrowser |
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