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 mr1783 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
vg0211295378 sf0211295375 2 11295378 5.25E-11 8.17E-06
vg0420200137 sf0420028179 4 20200137 1.78E-10 NA
vg0127205108 sf0127204064 1 27205108 2.32E-10 4.32E-06
vg0907961129 sf0907960129 9 7961129 2.88E-10 NA
vg0608184995 sf0608183996 6 8184995 4.02E-10 NA
vg0211220517 sf0211220514 2 11220517 6.51E-10 6.76E-06
vg0115899007 sf0115897981 1 15899007 3.68E-08 2.73E-06
vg0905075837 sf0905074837 9 5075837 NA 3.45E-06
vg1007900043 sf1007915653 10 7900043 NA 4.12E-06