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 mr1302 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
vg0400149978 sf0400148978 4 149978 8.47E-08 8.47E-08
vg0906637914 sf0906636914 9 6637914 2.76E-07 2.76E-07
vg0918774898 sf0918773898 9 18774898 4.15E-07 4.15E-07
vg0810864582 sf0810863587 8 10864582 2.35E-06 2.35E-06
vg0805095019 sf0805094022 8 5095019 2.71E-06 2.71E-06
vg1218825117 sf1218796552 12 18825117 3.00E-06 3.00E-06
vg0428761895 sf0428576746 4 28761895 3.24E-06 3.24E-06
vg0428141597 sf0427956461 4 28141597 3.87E-06 3.87E-06
vg0223074046 sf0223068177 2 23074046 3.96E-06 3.96E-06
vg0916031114 sf0916030113 9 16031114 4.59E-06 4.59E-06
vg0402377656 sf0402373251 4 2377656 4.81E-06 4.81E-06