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 mr1442 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
vg1200996819 sf1200995819 12 996819 3.60E-12 5.20E-06
vg0524837637 sf0524775052 5 24837637 4.48E-12 2.87E-06
vg0104046006 sf0104045006 1 4046006 8.54E-12 3.98E-06
vg0330358283 sf0330351322 3 30358283 9.46E-12 NA
vg0626322631 sf0626321634 6 26322631 1.56E-11 NA
vg0626189169 sf0626188172 6 26189169 3.39E-11 2.87E-07
vg1013341735 sf1013270505 10 13341735 1.48E-09 NA
vg0104000380 sf0103999380 1 4000380 7.92E-09 7.99E-07
vg0703513223 sf0703512224 7 3513223 1.45E-08 NA
vg1017085147 sf1017013919 10 17085147 NA 3.86E-07
vg1017210888 sf1017139661 10 17210888 NA 7.03E-07