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 mr1608 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
vg0216851136 sf0216845266 2 16851136 3.29E-21 1.91E-13
vg0217095683 sf0217089813 2 17095683 6.65E-21 3.63E-13
vg1220336226 sf1220307668 12 20336226 1.64E-12 6.99E-06
vg0406258553 sf0406253993 4 6258553 2.94E-11 NA
vg0216353266 sf0216347396 2 16353266 8.12E-11 2.82E-06
vg1108225523 sf1108220133 11 8225523 1.83E-10 NA
vg0216674769 sf0216668899 2 16674769 7.60E-08 6.75E-08
vg1019395575 sf1019324130 10 19395575 1.87E-07 1.03E-07
vg0702308497 sf0702307498 7 2308497 5.67E-07 NA
vg1109628487 sf1109623064 11 9628487 1.90E-06 NA
vg0324613061 sf0324611140 3 24613061 2.65E-06 4.60E-06
vg1019396556 sf1019325111 10 19396556 3.13E-06 5.36E-07
vg1204294396 sf1204293384 12 4294396 NA 1.95E-06