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 mr1806 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
vg1105470288 sf1105466039 11 5470288 1.12E-09 4.84E-06
vg0217951693 sf0217945824 2 17951693 1.51E-09 NA
vg1101949649 sf1101948649 11 1949649 2.28E-09 NA
vg0218031568 sf0218025699 2 18031568 4.75E-09 NA
vg1104978992 sf1104974803 11 4978992 6.63E-09 3.00E-06
vg0217846554 sf0217840685 2 17846554 1.11E-08 NA
vg0431614108 sf0431429003 4 31614108 1.26E-06 NA
vg0416544450 sf0416372491 4 16544450 1.33E-06 NA
vg0807470225 sf0807469230 8 7470225 1.40E-06 6.57E-07
vg0317962122 sf0317960904 3 17962122 7.94E-06 NA
vg1126137805 sf1125666219 11 26137805 NA 1.56E-06
vg0709361077 sf0709360083 7 9361077 NA 2.74E-06