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 mr1633 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
vg0205284721 sf0205284719 2 5284721 3.34E-15 1.52E-13
vg0205293173 sf0205293171 2 5293173 1.28E-09 2.13E-09
vg0726964336 sf0726963342 7 26964336 1.00E-08 NA
vg0402168068 sf0402163663 4 2168068 3.40E-08 1.94E-07
vg0141763299 sf0141762256 1 41763299 5.88E-08 NA
vg0607980327 sf0607979328 6 7980327 8.42E-07 7.75E-07
vg1214775081 sf1214772422 12 14775081 1.92E-06 9.65E-07
vg0608005446 sf0608004447 6 8005446 NA 2.42E-06