Detailed information of SNP:



SNP ID: sf0402088806(Gbrowse)

Chromosome: chr04

Position: 2088806
Major allele: C

Minor allele: T

Reference allele: T

Allele Frequencies:


NOTE: The detailed information of the classification of populations can be found in the "Notes and Data Evaluation" page.


PopulationsPopulation SizeFrequency of C(major allele)Frequency of T(minor allele)
All1389 77.39% 22.61%
All Indica777 86.62% 13.38%
All Japonica493 60.45% 39.55%
Aus67 92.54% 7.46%
Indica I361 82.55% 17.45%
Indica II211 93.36% 6.64%
Indica Intermediate205 86.83% 13.17%
Temperate Japonica334 48.80% 51.20%
Tropical Japonica93 90.32% 9.68%
Japonica Intermediate66 77.27% 22.73%
Group VI/Aromatic14 64.29% 35.71%
Intermediate38 86.84% 13.16%

Allele Var Effect:


SNP ID Var Gene Effect/Location
sf0402088806 T->C LOC_Os04g04400(LOC_Os04g04400.1) INTRON