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 mr1393 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
vg1212214384 sf1212211722 12 12214384 6.47E-07 6.47E-07
vg0327345253 sf0327338306 3 27345253 6.90E-07 6.90E-07
vg0315007040 sf0315005687 3 15007040 1.00E-06 1.00E-06
vg1216247174 sf1216244470 12 16247174 1.41E-06 1.41E-06
vg1003719342 sf1003718319 10 3719342 3.26E-06 3.26E-06
vg1121337815 sf1120871692 11 21337815 4.31E-06 4.31E-06
vg0226215115 sf0226209246 2 26215115 4.82E-06 4.82E-06