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 mr1336 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
vg0727265567 sf0727264573 7 27265567 1.57E-22 5.48E-06
vg0231858637 sf0231852768 2 31858637 4.94E-22 NA
vg0326930070 sf0326923123 3 26930070 5.12E-22 NA
vg1203474916 sf1203473916 12 3474916 5.77E-22 NA
vg0226148109 sf0226142240 2 26148109 7.46E-22 NA
vg1103160376 sf1103156279 11 3160376 5.64E-19 NA
vg0716104334 sf0716103341 7 16104334 9.66E-18 NA
vg1122865112 sf1122398983 11 22865112 NA 4.41E-06