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 mr1268 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
vg1216282319 sf1216279615 12 16282319 3.26E-09 7.83E-08
vg1128243970 sf1127720749 11 28243970 3.38E-08 7.32E-06
vg1216274089 sf1216271385 12 16274089 5.44E-08 2.25E-06
vg1219486552 sf1219458022 12 19486552 8.14E-08 2.45E-06
vg1207069483 sf1207068373 12 7069483 8.50E-08 NA
vg0913504480 sf0913503479 9 13504480 4.48E-07 4.31E-06
vg0501563153 sf0501563137 5 1563153 6.68E-07 2.43E-06
vg0805516079 sf0805515082 8 5516079 9.68E-07 1.12E-06
vg0706405260 sf0706404265 7 6405260 1.02E-06 2.69E-07
vg0807735012 sf0807734017 8 7735012 1.23E-06 1.90E-06
vg1108921957 sf1108916567 11 8921957 1.54E-06 9.51E-07
vg0601176961 sf0601175962 6 1176961 3.13E-06 1.17E-06