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 mr1779 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
vg0308476883 sf0308475821 3 8476883 7.77E-08 7.77E-08
vg0721179505 sf0721178512 7 21179505 3.56E-07 3.56E-07
vg0330523640 sf0330516529 3 30523640 3.98E-07 3.98E-07
vg0414348721 sf0414339434 4 14348721 1.52E-06 1.52E-06
vg1218112515 sf1218083951 12 18112515 1.75E-06 1.75E-06
vg0721449575 sf0721448582 7 21449575 2.54E-06 2.54E-06
vg0209482698 sf0209482696 2 9482698 2.96E-06 2.96E-06
vg0314035630 sf0314034319 3 14035630 4.57E-06 4.58E-06
vg0126579920 sf0126578876 1 26579920 4.94E-06 4.94E-06
vg0113113581 sf0113112555 1 13113581 5.00E-06 5.00E-06