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 mr1151 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
vg0900280507 sf0900279507 9 280507 8.32E-07 8.32E-07
vg1121751063 sf1121284940 11 21751063 1.18E-06 1.18E-06
vg1127608750 sf1127137137 11 27608750 1.99E-06 1.99E-06
vg0715414736 sf0715413743 7 15414736 1.99E-06 2.00E-06
vg0141571889 sf0141570846 1 41571889 2.52E-06 2.52E-06
vg0918511304 sf0918510303 9 18511304 2.63E-06 2.63E-06
vg1117569414 sf1117103271 11 17569414 3.86E-06 3.86E-06
vg0115129673 sf0115128647 1 15129673 4.41E-06 4.41E-06