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 mr1325 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
vg0217855786 sf0217849917 2 17855786 1.77E-07 1.77E-07
vg1214590110 sf1214587450 12 14590110 1.99E-06 1.99E-06
vg1216728500 sf1216722454 12 16728500 2.37E-06 2.37E-06
vg1014017091 sf1013945857 10 14017091 2.60E-06 2.60E-06
vg0118829535 sf0118828490 1 18829535 2.94E-06 2.94E-06
vg1208155262 sf1208152668 12 8155262 4.44E-06 4.45E-06
vg0208434103 sf0208434102 2 8434103 4.79E-06 4.80E-06
vg0726431700 sf0726430706 7 26431700 8.22E-06 8.22E-06