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 mr1864 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
vg0419230999 sf0419059037 4 19230999 1.80E-22 6.67E-19
vg1209987334 sf1209984745 12 9987334 1.46E-09 NA
vg1217913079 sf1217884513 12 17913079 1.17E-08 NA
vg0417353746 sf0417181789 4 17353746 4.70E-08 2.67E-06
vg1207186403 sf1207183793 12 7186403 7.10E-08 NA
vg0417381371 sf0417209414 4 17381371 7.71E-08 1.72E-06
vg1209892012 sf1209889422 12 9892012 8.09E-08 2.68E-06
vg1223453137 sf1223419597 12 23453137 NA 2.34E-06
vg1112989462 sf1112525783 11 12989462 NA 4.05E-06
vg0318751093 sf0318749853 3 18751093 NA 4.59E-06