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 mr1525 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
vg0405913502 sf0405908943 4 5913502 4.67E-10 5.19E-09
vg0405727386 sf0405722825 4 5727386 1.10E-09 2.67E-08
vg0405539763 sf0405535204 4 5539763 3.19E-09 7.74E-09
vg0405598798 sf0405594239 4 5598798 1.45E-07 8.87E-08
vg0620080444 sf0620079447 6 20080444 4.84E-07 4.63E-06
vg0401247884 sf0401243434 4 1247884 9.97E-07 8.28E-07
vg0401247859 sf0401243409 4 1247859 2.52E-06 3.93E-06
vg1121614615 sf1121148492 11 21614615 2.79E-06 1.99E-06
vg0401154788 sf0401150338 4 1154788 NA 4.00E-06
vg1225863791 sf1225830186 12 25863791 NA 7.24E-06