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 mr1545 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
vg0129451214 sf0129450169 1 29451214 4.06E-10 6.92E-07
vg1210709667 sf1210707080 12 10709667 4.64E-09 7.17E-07
vg0130555317 sf0130554273 1 30555317 4.29E-08 NA
vg0909394179 sf0909393178 9 9394179 1.89E-06 3.44E-07
vg0123927172 sf0123926128 1 23927172 6.72E-06 NA