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 mr1449 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
vg0803439483 sf0803438486 8 3439483 8.07E-10 2.12E-06
vg0333461136 sf0333454006 3 33461136 1.11E-09 1.17E-06
vg0804724828 sf0804723831 8 4724828 1.90E-09 2.92E-06
vg0434561028 sf0434375920 4 34561028 6.43E-09 NA
vg0135080963 sf0135079920 1 35080963 1.08E-08 NA