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 mr1850 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
vg0610182858 sf0610181859 6 10182858 5.30E-08 5.30E-08
vg1213210547 sf1213207885 12 13210547 4.04E-07 4.04E-07
vg0529112100 sf0529049455 5 29112100 6.79E-07 6.79E-07
vg0602130119 sf0602129120 6 2130119 1.00E-06 1.00E-06
vg0714048670 sf0714047677 7 14048670 1.48E-06 1.49E-06
vg0721416115 sf0721415122 7 21416115 1.49E-06 1.49E-06
vg0204550077 sf0204550074 2 4550077 1.79E-06 1.79E-06
vg0204546811 sf0204546808 2 4546811 2.12E-06 2.12E-06
vg0610547852 sf0610546853 6 10547852 3.52E-06 3.52E-06
vg0220268633 sf0220262765 2 20268633 4.82E-06 4.82E-06