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 mr1457 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
vg1218514358 sf1218485794 12 18514358 3.74E-32 2.96E-10
vg1218592795 sf1218564231 12 18592795 5.23E-30 9.53E-12
vg0106827714 sf0106826714 1 6827714 9.97E-22 NA
vg0702715981 sf0702714982 7 2715981 1.52E-21 NA
vg0141073686 sf0141072643 1 41073686 3.41E-21 NA
vg1204422933 sf1204421921 12 4422933 3.77E-21 NA
vg0404380761 sf0404376365 4 4380761 1.38E-16 NA
vg0421021694 sf0420849747 4 21021694 2.10E-16 NA
vg0727982897 sf0727981904 7 27982897 NA 1.09E-09
vg1218852237 sf1218823672 12 18852237 NA 2.61E-07
vg1218590388 sf1218561824 12 18590388 NA 2.78E-07
vg1218107426 sf1218078862 12 18107426 NA 1.03E-06
vg1218493508 sf1218464944 12 18493508 NA 1.39E-06
vg0728019959 sf0728018966 7 28019959 NA 2.68E-06
vg0817796326 sf0817793613 8 17796326 NA 3.09E-06
vg0728762565 sf0728761573 7 28762565 NA 4.08E-06