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 mr1584 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
vg1019363923 sf1019292478 10 19363923 2.75E-10 NA
vg1216542519 sf1216539812 12 16542519 1.13E-09 NA
vg0801815194 sf0801814197 8 1815194 1.64E-09 NA
vg1019960269 sf1019888769 10 19960269 4.04E-09 NA
vg0518422633 sf0518362119 5 18422633 4.59E-09 NA
vg0313147221 sf0313145939 3 13147221 6.74E-09 NA
vg1215484344 sf1215481641 12 15484344 7.97E-09 NA
vg0502242174 sf0502242149 5 2242174 3.61E-07 NA