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 mr1320 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
vg0818577415 sf0818574702 8 18577415 4.06E-10 NA
vg0420767744 sf0420595787 4 20767744 5.12E-10 NA
vg0701136340 sf0701135340 7 1136340 8.88E-10 NA
vg0328375479 sf0328368532 3 28375479 9.76E-10 NA
vg0623104065 sf0623103068 6 23104065 1.17E-09 NA
vg0701084978 sf0701083978 7 1084978 5.90E-09 NA
vg0502159367 sf0502159342 5 2159367 2.51E-08 5.11E-06
vg0406860866 sf0406856311 4 6860866 NA 6.04E-07
vg1107376701 sf1107372446 11 7376701 NA 1.52E-06
vg0212145917 sf0212145913 2 12145917 NA 2.86E-06