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 mr1448 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
vg1208521115 sf1208518522 12 8521115 6.66E-39 3.40E-06
vg0205678863 sf0205678863 2 5678863 7.60E-39 NA
vg0500744790 sf0500744790 5 744790 8.18E-39 NA
vg0805525338 sf0805524341 8 5525338 8.21E-39 NA
vg0113689599 sf0113688573 1 13689599 1.02E-38 NA
vg0809104762 sf0809103766 8 9104762 NA 3.24E-07
vg0327967882 sf0327960936 3 27967882 NA 1.05E-06
vg0119127859 sf0119126814 1 19127859 NA 1.16E-06
vg0327926363 sf0327919417 3 27926363 NA 1.56E-06
vg0327930050 sf0327923104 3 27930050 NA 2.21E-06
vg0823588721 sf0823586007 8 23588721 NA 4.04E-06
vg0400763214 sf0400762214 4 763214 NA 5.75E-06
vg0419905615 sf0419733651 4 19905615 NA 9.67E-06