Single-locus model
- In the SNP mode of Single-locus page, different genetic variant loci are visually displayed below the gene structure diagram. Users can click on various loci to view detailed information and determine if the locus is significantly associated with the expression of the gene.
- Furthermore, we developed the Haplotype mode. Users can select different haplotypes to obtain correlations with gene expression.
- The raw transcriptome data utilized in AMIR is sourced from publicly accessible databases. It is imperative for researchers to accurately cite the original sources when employing this data in their work（see Reference）
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Basic information about the searched gene(s)
| Gene ID | Species | AtGI/Name | Position | Seq/Exp | SNPs No. | SNP No.(High/Moderate/Low/Modifier) |
|---|
Gene structure and SNP distribution
The inverted triangle symbols indicate variations, click it to see detailed information in table.
Annotation and statistics of SNPs
Information of SNPs(Alt greater than 0) in
PIC: polymorphism information content
| Selector | Chr. | Position | Alt (allele) | Ref (allele) | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
|---|
Information of SNPs in and its ± kb flanking region
PIC: polymorphism information content
| Chr. | Position | Alt (allele) | Ref (allele) | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
|---|
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 |
|---|
Information of samples
| Type | PRJNA | Cultivar | SRR | Species | Tissue | Treatment | Description | Ref |
|---|
Expression of
p-value: (t-test); (wilcoxon-test)
| Selector | Chr. | Position | Alt (allele) | Ref (allele) | Alt (frequency) | Ref (frequency) | PIC | Alt (num) | Ref (num) | Function type | Variation type | Functional annotations |
|---|
| ID | Haplotype | Frequency | Sample |
|---|