Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1515 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0628893075 sf0628892077 6 28893075 6.15E-09 NA
vg0411398819 sf0411389522 4 11398819 1.35E-08 NA
vg0406221879 sf0406217319 4 6221879 1.38E-08 NA
vg1002941120 sf1002940097 10 2941120 3.31E-08 1.54E-07
vg0406868775 sf0406864220 4 6868775 8.43E-08 NA
vg0235115955 sf0235110086 2 35115955 1.58E-07 3.11E-06
vg0726555808 sf0726554814 7 26555808 2.34E-06 NA
vg0406033822 sf0406029261 4 6033822 2.67E-06 4.96E-06
vg0208482033 sf0208482032 2 8482033 5.73E-06 NA