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 mr1064 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
vg1210215832 sf1210213244 12 10215832 1.23E-10 NA
vg1209209246 sf1209206655 12 9209246 4.22E-10 2.66E-06
vg0217787880 sf0217782011 2 17787880 1.29E-09 3.61E-06
vg0129380015 sf0129378970 1 29380015 2.33E-09 3.57E-06
vg1224020476 sf1223986929 12 24020476 2.62E-09 NA
vg1215976911 sf1215974207 12 15976911 3.15E-09 NA
vg0619826206 sf0619825209 6 19826206 4.74E-08 3.06E-06
vg0617787176 sf0617786179 6 17787176 2.24E-06 5.87E-06
vg1117166999 sf1116700851 11 17166999 9.55E-06 NA
vg0235590636 sf0235584767 2 35590636 NA 1.65E-06
vg1207890498 sf1207887904 12 7890498 NA 2.08E-06
vg0315064182 sf0315062829 3 15064182 NA 2.27E-06
vg0821203177 sf0821200464 8 21203177 NA 3.87E-06