Custom Genotyping and Comment Page

In custom call genotype page, ① and ③ query is ultimately using a region.

Custom query can reflect through four aspects:

①: You can set the upstream and downstream region of a locus.

②: You can choose any region or a position on the genome to query and genotyping. The region of chromosome fragment much no more than 20kb.

④: You can filtered population through three methods , detail see section "Population Selection".

⑤: You can filtered variation sites through set a variety of options, such as  allele type, frequency, depth, quality, and so on. After genotyping, you can choose the location of the variation site base on gene structure or manually check for recall genotype, detail see section "Region Structure and Genotype".

Population Select

This population filter module provides three methods of screening:

①: Select population according to project sources, the type of subgroup (support multiple),  and the quality of sample sequencing and mapping.

②: Select population through specific phenotype characteristics, click "Show Filter" button display the "Search by Phenotype" module, detail see below.

③: You can choose any region on the genome to query and genotyping. The region of chromosome fragment much in range 0.1 ~ 20kb.

② Select population by phenotype:

step 1:  Click  phenotype "Show Filter" button

step 2:  Select  phenotype name,  set filter rule of this phenotype, add "AND" or "OR" group in corresponding "Rule Inside“, set ”Rule Outside“ if need be.

step 3:  Click "Use Filter" button will apply all filter rules, the filtered sample number will display in the summary.

step 4:  Click "Changer" button, intersection of filtered population in "summary" will use for genotyping.

③: Select population from SNP-Tree:

step 1:  Click  SNP-Tree "Show Filter" button

step 2:  Select sample by click parent-node in tree, all the leaf-node (sample) of selected parent-node will be use for genotyping. Selected parent-node show in above with red font, and use "" marked in tree.  You can deselect the parent-node by click again.

step 3:  Click "Use Select" button will apply all selected sample, and the sample number will display in the summary.

step 4:  Click "Changer" button, intersection of filtered population in "summary" will use for genotyping.

Region Structure and Genotype

This module is used to show gene structure and other annotation stracks (now, only have domain track). Mouse Hovering over a rectangular structure will show detailed information of this part.  

    If you want to use a locus for querying (ex. LOC_Os01g01280), only this locus gene should be showed in the gene structure view. If the query is using a genomic region (ex. Chr1:134291..135685), all annotation locus gene of this area will be show in the view (above).

    A typical eukaryotic gene including 5'UTR (orange), exon (blue), intron and 3'UTR (green). Click and select a locus mRNA ID (), the coding amino acid sequence of this mRNA will be displayed in sequence view window with black background (REF, reference DNA sequences.  AA, amino acid sequences). Meanwhile, the background color of variation position row (③) is also corresponding to change, in genotype table below. So that it can easily detect mutations which took place in exons.

How can we predict the effect of different genotypes on reference protein's function?

step : Click mRNA ID in gene structure view to select the protein as a reference. This reference protein sequence will be displayed in sequence view.

step : Click genotype row that you want to analyze in genotype table. The genotype may contain a set of SNP and InDel, that maybe change the structure of protein, but the analysis of effect is as an integrated whole, not a separate. modified amino acid sequence will display corresponding in the sequence view.

step : Click variation sites that you want to check in the position row, Ex. click position 295 (152259),  the sequence window and chromosome cursor will automatically jump to the corresponding position, As shown in figure this mutation site resulted in the substitution of amino acids (AG).

step : Drag the cursor chromosomes, can view the other position change of amino acid sequence.

How to use the custom recall control?

Sample Num: change the value, click the "Changer" buttons recall genotype, only affect the number of genotypes.

ALT Frequency (and more): change the value,  click the "Changer" buttons, filter eligible mutation loci, the number and location of genotype number will change.

ReCall: first select mRNA ID in gene structure view,  second check the boxes associated with structural unit listed, finally click "ReCall" button recall genotype.

Custom Position: first click "Choice" button (this button will switch into "ReCall" and add check-box in each position in table),  second check the boxes in position row, finally click "ReCall" button recall genotype.

Merge: set the value of similarity, click the button will merge similar genotypes in the table that greater than the threshold.

How to add verified functional comment for a variation?

A proven mutations must have corresponding experimental evidence or WAGS results support, the different alleles must have obvious differences in phenotype.

We welcome website visitors and the author of the variation study to submit the annotation of relevant site, the annotation are open, but the annotation will be manually checked by website manager, the checked variations will be listed in the KnownGenes home page.

Click variation position in 'Genotype Table' () will pop the comments page (below), a annotated position will be marked with red color font.

Phenotype Box Plot

This module shows the genotype and phenotype correlation box plot.  You can choose interested phenotype from the floating menu for correlation analysis.

For each genotype box, move mouse over on will show detail number of sample and values. In this figure only show 15 genotypes (T1 - T15), Other genotype will co-movement display when click next page in above genotype table.

RNA-seq Expression

This module display gene expression profiles of query region, the values come from more than 400 RNA-Seq datasets that collected from NCBI, and those datasets belong to different tissue and development stage.

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