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 mr1780 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
vg1215983100 sf1215980396 12 15983100 1.57E-10 3.22E-06
vg1210583941 sf1210581354 12 10583941 3.16E-10 6.08E-07
vg1219373193 sf1219344662 12 19373193 1.17E-09 NA
vg1215994922 sf1215992218 12 15994922 1.59E-09 1.35E-06
vg1211970311 sf1211967646 12 11970311 1.12E-08 1.17E-06
vg0215801821 sf0215795951 2 15801821 3.25E-08 NA
vg1022580961 sf1022509435 10 22580961 1.12E-06 5.96E-06