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 mr1815 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
vg0316819218 sf0316818092 3 16819218 3.99E-06 1.90E-06
vg0229966285 sf0229960416 2 29966285 4.54E-06 1.84E-06
vg0432040936 sf0431855829 4 32040936 5.61E-06 NA
vg0623456853 sf0623455856 6 23456853 NA 1.59E-06
vg0233901685 sf0233895816 2 33901685 NA 3.03E-06