Genotype Home Page Search Box


There are four query mode , and two links to the page of advanced function.

①: Query Locus genotype by ID, the Locus genotype have been called using all high cover population sample with the default parameters (SNP/InDel allele frequency >0.15%), the query result will be displayed in a new page, detail see topic "Locus Genotype".

②: Click "Advanced" will link to "Custom Call Genotype" function page.

③: Get all genotype of one germplasm, Query by germplasm or sample name, the result will be displayed in a new page, detail see topic "Germplasm Genotype".

④: Click "Compare" will link to "Genotype Compare" function page.

⑤: Search all population SNP/InDel by given chromosome range and option, the result will be list in below table, detail see below "SNP/InDel Search Result".

⑥: Search unified Locus by given chromosome range and option, the result will be list in below table, detail see below "Locus Search Result". GT Num,  genotype number.  Named Gene, gene with symbol annotation. Traits gene, gene with description of related phenotype.



SNP/InDel Search Result


REF: The base of the reference sequence.

ALT:  Allele, "-" mean missing values.

AN:  Allele number.

AC:  Allele count.

AF:  Allele frequency,  AF= AC / AN,  but "-" frequency = "-" number / total sample number



Locus Search Result


Locus ID: Unified Locus ID in our database, this locus module detail see genotype home summary.

GT Num:  genotype number of this unified locus which genotype calling used Nip as reference genome

Click "Locus ID" link to  "Locus Genotype" page.

Click "Region" or "Source ID" link to "Custom Call Genotype" function page.

①: Provide a filter function base on Locus Note.

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