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 mr1931 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
vg0427992657 sf0427807521 4 27992657 4.80E-11 NA
vg0627297348 sf0627296351 6 27297348 9.63E-10 NA
vg0701301806 sf0701300806 7 1301806 2.24E-09 NA
vg0610115996 sf0610114997 6 10115996 2.33E-09 NA
vg0324692311 sf0324690390 3 24692311 3.40E-09 NA
vg0617688888 sf0617687891 6 17688888 1.42E-07 3.25E-06
vg1215554899 sf1215552196 12 15554899 9.64E-07 NA
vg1203659267 sf1203658266 12 3659267 1.19E-06 NA
vg0904123337 sf0904122337 9 4123337 5.68E-06 NA
vg1208638106 sf1208635513 12 8638106 8.56E-06 1.86E-06