Detailed information of SNP:



SNP ID: sf0500201539(Gbrowse)

Chromosome: chr05

Position: 201539
Major allele: T

Minor allele: C

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 T(major allele)Frequency of C(minor allele)
All1419 95.84% 4.16%
All Indica799 96.12% 3.88%
All Japonica497 99.80% 0.20%
Aus67 59.70% 40.30%
Indica I375 99.20% 0.80%
Indica II213 88.26% 11.74%
Indica Intermediate211 98.58% 1.42%
Temperate Japonica335 100.00% 0.00%
Tropical Japonica94 100.00% 0.00%
Japonica Intermediate68 98.53% 1.47%
Group VI/Aromatic14 100.00% 0.00%
Intermediate42 100.00% 0.00%

Allele Var Effect:


SNP ID Var Gene Effect/Location
sf0500201539 T->C LOC_Os05g01310(LOC_Os05g01310.2) UTR_5_PRIME
sf0500201539 T->C LOC_Os05g01310(LOC_Os05g01310.1) UTR_5_PRIME
sf0500201539 T->C LOC_Os05g01310(LOC_Os05g01310.3) UTR_5_PRIME