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 mr1585 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
vg0217108340 sf0217102470 2 17108340 1.05E-10 1.24E-06
vg0216789715 sf0216783845 2 16789715 1.06E-10 4.23E-09
vg1202009958 sf1202008956 12 2009958 4.00E-07 1.30E-06
vg1010067602 sf1009996423 10 10067602 4.92E-07 5.04E-06
vg1125675581 sf1125209420 11 25675581 1.62E-06 NA
vg0216664819 sf0216658949 2 16664819 2.90E-06 8.14E-07
vg0217323055 sf0217317185 2 17323055 8.49E-06 1.58E-06
vg1119998277 sf1119532200 11 19998277 NA 4.83E-06