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 mr1256 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
vg0222726563 sf0222720694 2 22726563 5.96E-14 2.87E-12
vg0224127834 sf0224121965 2 24127834 1.45E-09 2.80E-08
vg0224137364 sf0224131495 2 24137364 8.04E-07 1.34E-06
vg0509011910 sf0509011838 5 9011910 2.15E-06 2.39E-06
vg0709664645 sf0709663651 7 9664645 4.28E-06 2.26E-06
vg0513252916 sf0513195838 5 13252916 4.39E-06 3.38E-06
vg0406854976 sf0406850421 4 6854976 5.29E-06 7.07E-07
vg0615270938 sf0615269939 6 15270938 6.45E-06 7.00E-06