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 mr1570 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
vg0609098355 sf0609097356 6 9098355 1.95E-12 1.37E-08
vg0608672147 sf0608671148 6 8672147 2.51E-12 4.41E-09
vg0431905664 sf0431720559 4 31905664 1.84E-08 NA
vg1207140697 sf1207139587 12 7140697 5.58E-08 NA
vg0407590794 sf0407586062 4 7590794 5.81E-08 NA
vg0207991663 sf0207991662 2 7991663 3.16E-07 4.36E-08
vg1126583106 sf1126111521 11 26583106 2.58E-06 NA
vg0906051911 sf0906050911 9 6051911 4.88E-06 3.89E-06
vg1119554312 sf1119088000 11 19554312 NA 2.96E-06
vg0135957843 sf0135956800 1 35957843 NA 4.08E-06