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 mr1231 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
vg0305036157 sf0305035159 3 5036157 9.93E-19 NA
vg0724568778 sf0724567784 7 24568778 1.71E-17 NA
vg0329929930 sf0329922969 3 29929930 1.86E-17 NA
vg0129940783 sf0129939738 1 29940783 1.88E-17 NA
vg0205899984 sf0205899984 2 5899984 2.47E-17 NA
vg0918924003 sf0918923003 9 18924003 1.06E-14 2.52E-09
vg0918496669 sf0918495668 9 18496669 NA 1.10E-07
vg1215465887 sf1215463184 12 15465887 NA 9.56E-07
vg1020343288 sf1020271768 10 20343288 NA 1.10E-06
vg0322556933 sf0322555422 3 22556933 NA 2.09E-06
vg0621676444 sf0621675447 6 21676444 NA 2.40E-06
vg0908683598 sf0908682597 9 8683598 NA 3.04E-06
vg0906170235 sf0906169235 9 6170235 NA 3.24E-06