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 mr1470 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
vg0224408464 sf0224402595 2 24408464 1.32E-09 1.32E-09
vg0224109596 sf0224103727 2 24109596 9.11E-09 9.11E-09
vg0911270881 sf0911269880 9 11270881 6.36E-08 6.36E-08
vg0224459717 sf0224453848 2 24459717 1.07E-07 1.07E-07
vg0224284161 sf0224278292 2 24284161 5.68E-07 5.68E-07
vg1000062161 sf1000061161 10 62161 1.36E-06 1.36E-06
vg0224219685 sf0224213816 2 24219685 1.52E-06 1.52E-06
vg0209830497 sf0209830495 2 9830497 2.90E-06 2.90E-06
vg1000066190 sf1000065190 10 66190 3.74E-06 3.74E-06
vg0123862783 sf0123861739 1 23862783 7.32E-06 7.33E-06