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 mr1897 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
vg0217145884 sf0217140014 2 17145884 6.47E-39 6.12E-23
vg0217095683 sf0217089813 2 17095683 7.71E-39 2.24E-25
vg1108225523 sf1108220133 11 8225523 4.87E-18 5.52E-07
vg1216728961 sf1216722915 12 16728961 1.26E-15 1.29E-06
vg0212591710 sf0212591706 2 12591710 3.83E-15 1.14E-07
vg1220336402 sf1220307844 12 20336402 6.48E-14 NA
vg1216728974 sf1216722928 12 16728974 1.06E-12 4.20E-06
vg1216728542 sf1216722496 12 16728542 1.08E-11 6.87E-07
vg0216409820 sf0216403950 2 16409820 2.16E-11 1.01E-07
vg0213232689 sf0213232685 2 13232689 8.03E-11 2.22E-07
vg0218852605 sf0218846736 2 18852605 1.11E-10 1.75E-06
vg1216723603 sf1216717557 12 16723603 1.78E-10 9.22E-08
vg0217324261 sf0217318391 2 17324261 6.28E-09 3.30E-10
vg0427400065 sf0427214929 4 27400065 1.94E-07 5.39E-07
vg0421518167 sf0421346218 4 21518167 2.05E-07 6.27E-07
vg0421509835 sf0421337886 4 21509835 4.39E-07 5.19E-07
vg0427400029 sf0427214893 4 27400029 3.55E-06 2.50E-07
vg0224604930 sf0224599061 2 24604930 NA 1.54E-06
vg1004552820 sf1004569358 10 4552820 NA 2.98E-06