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 mr1721 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
vg1001390120 sf1001389097 10 1390120 2.39E-15 4.87E-11
vg1001385051 sf1001384028 10 1385051 5.27E-15 3.33E-12
vg0720057906 sf0720056913 7 20057906 5.21E-10 5.03E-07
vg1001637985 sf1001636962 10 1637985 1.30E-09 1.63E-07
vg0715644976 sf0715643983 7 15644976 2.48E-09 NA
vg1001096915 sf1001095891 10 1096915 6.47E-09 NA
vg1001639869 sf1001638846 10 1639869 2.62E-07 2.20E-06
vg0804589533 sf0804588536 8 4589533 2.41E-06 2.57E-06
vg0421979686 sf0421807737 4 21979686 8.22E-06 2.52E-06
vg0906482532 sf0906481532 9 6482532 NA 2.60E-06
vg0203225917 sf0203225915 2 3225917 NA 6.53E-06