Locus Genotype Page

This independent page URL:{species}/genotype/byLocus/{Locus ID}

{species} : species name, such as "rice".

{Locus ID}: Unified locus ID (ex. OsG00000081) or Source ID (Os01g0102900).

This page  includes four model:

  • Base Information
  • Genotype Show
  • Genotype Component
  • Phenotype Box Plot
  • Locus RNA-seq Expression

Base Information

Change the reference genome in drop-down list, all content of the page will change, because the genotyping results is differences based on different reference genome.

Total GT Num: total genotype number which call genotype using all population sample.

Retained GT Num: genotype which contains sample numbers more than 10.

Genotype Show

GT_ID: genotype ID of this unified locus (OsG00000081), click ID will link to a corresponding new page, detail see  "Genotype Detail".

Sample Num: the number of samples with the same genotype.

Variants Position =  offset(k)*1000 + position.

REF:  row 3, base of the reference sequence. Mouse hovering will show allele frequency.

In REF row, chart 'N' represents multiple continuous bases, which means the variation of this position for corresponding sample is deletion, in genotype row, the 'N' represents insertion of bases.

In genotype row, capital base means this position variation is homozygous, lowercase is heterozygous.

Genotype Component

This stacked car chart displays subgroup component of samples for each genotype. Mouse hovering will show the detail of the subgroup.

There are three subgroup classification methods can be choose:

SG: Variety group based on SNP phylogenetic analyses.

VG: Variety group based on the morphologic features.

ORI: Origin country of samples

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.

Created with the Personal Edition of HelpNDoc: Create help files for the Qt Help Framework