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 mr1285 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
vg0402237717 sf0402233312 4 2237717 2.07E-09 1.83E-06
vg1117476915 sf1117010770 11 17476915 4.09E-09 NA
vg1127790110 sf1127318496 11 27790110 6.95E-09 2.54E-08
vg0316224648 sf0316223296 3 16224648 5.04E-08 NA
vg1124625149 sf1124158989 11 24625149 7.57E-08 NA
vg0407243554 sf0407238824 4 7243554 3.43E-06 NA
vg0714405504 sf0714404511 7 14405504 3.74E-06 NA
vg0525520857 sf0525458278 5 25520857 8.00E-06 NA
vg1218068686 sf1218040122 12 18068686 NA 1.90E-06