Detailed information of SNP:



SNP ID: sf0401704588(Gbrowse)

Chromosome: chr04

Position: 1704588
Major allele: T

Minor allele: C

Reference allele: C

Allele Frequencies:


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


PopulationsPopulation SizeFrequency of T(major allele)Frequency of C(minor allele)
All1418 54.09% 45.91%
All Indica798 74.56% 25.44%
All Japonica497 24.35% 75.65%
Aus67 26.87% 73.13%
Indica I375 70.67% 29.33%
Indica II212 78.77% 21.23%
Indica Intermediate211 77.25% 22.75%
Temperate Japonica335 27.76% 72.24%
Tropical Japonica94 15.96% 84.04%
Japonica Intermediate68 19.12% 80.88%
Group VI/Aromatic14 78.57% 21.43%
Intermediate42 52.38% 47.62%

Allele Var Effect:


SNP ID Var Gene Effect/Location
sf0401704588 C->T LOC_Os04g03796(LOC_Os04g03796.2) INTRON
sf0401704588 C->T LOC_Os04g03796(LOC_Os04g03796.1) INTRON