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 mr1617 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
vg0604350087 sf0604349088 6 4350087 1.43E-26 8.93E-18
vg0913424446 sf0913423445 9 13424446 8.11E-14 NA
vg0207150816 sf0207150816 2 7150816 1.32E-13 NA
vg1000509880 sf1000508856 10 509880 4.59E-13 NA
vg1022854220 sf1022782693 10 22854220 6.47E-13 NA
vg1123185842 sf1122714954 11 23185842 5.21E-12 5.29E-06
vg0604373917 sf0604372918 6 4373917 5.84E-09 8.21E-10