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 mr1024 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
vg1101960396 sf1101959396 11 1960396 1.77E-12 NA
vg1207212131 sf1207209525 12 7212131 1.14E-11 6.50E-07
vg1215337617 sf1215334915 12 15337617 2.46E-11 NA
vg1207220776 sf1207218172 12 7220776 5.12E-11 1.58E-06
vg1207539306 sf1207536712 12 7539306 9.12E-11 5.46E-07
vg1207110670 sf1207109560 12 7110670 4.21E-10 1.41E-06
vg1207114214 sf1207113104 12 7114214 4.81E-10 6.44E-07
vg1219558340 sf1219529810 12 19558340 1.35E-09 NA
vg1206807863 sf1206806753 12 6807863 1.15E-07 NA
vg0720364932 sf0720363939 7 20364932 2.15E-07 1.51E-06
vg1121615697 sf1121149574 11 21615697 3.83E-07 4.81E-06