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 mr1281 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
vg1126786095 sf1126314482 11 26786095 1.26E-07 9.91E-07
vg0211330175 sf0211330172 2 11330175 2.42E-07 1.99E-07
vg1117523173 sf1117057028 11 17523173 1.01E-06 1.67E-07
vg1016070140 sf1015998912 10 16070140 1.74E-06 2.02E-06
vg0220806690 sf0220800822 2 20806690 2.17E-06 4.68E-06
vg1205541281 sf1205540267 12 5541281 3.01E-06 4.21E-06