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 mr1422 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
vg0610251688 sf0610250689 6 10251688 2.71E-20 1.79E-12
vg0629122924 sf0629121926 6 29122924 3.40E-10 2.91E-06
vg0610487198 sf0610486199 6 10487198 2.94E-09 2.58E-06
vg0706098977 sf0706097978 7 6098977 1.14E-08 NA
vg0705176208 sf0705175209 7 5176208 2.24E-08 NA
vg1117484782 sf1117018637 11 17484782 4.08E-07 NA
vg0610421076 sf0610420077 6 10421076 1.60E-06 4.17E-06
vg0921359314 sf0921358833 9 21359314 6.24E-06 1.62E-06