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 mr1370 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
vg0630078359 sf0630077361 6 30078359 2.04E-07 2.05E-07
vg1108503687 sf1108498297 11 8503687 1.32E-06 1.32E-06
vg1005078438 sf1005094975 10 5078438 2.13E-06 2.13E-06
vg0105137583 sf0105136583 1 5137583 3.15E-06 3.15E-06
vg0916184725 sf0916183724 9 16184725 3.92E-06 3.92E-06
vg0622464766 sf0622463769 6 22464766 4.91E-06 4.92E-06
vg1124408117 sf1123941961 11 24408117 4.93E-06 4.94E-06
vg1215653812 sf1215651109 12 15653812 9.02E-06 9.00E-06