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 mr1304 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
vg0728265516 sf0728264524 7 28265516 6.71E-14 2.05E-07
vg0129442068 sf0129441023 1 29442068 7.04E-13 3.68E-07
vg0706461994 sf0706460999 7 6461994 1.19E-11 NA
vg0506365010 sf0506364949 5 6365010 1.46E-11 NA
vg1202865605 sf1202864607 12 2865605 1.95E-11 NA
vg0223262220 sf0223256351 2 23262220 7.20E-11 1.73E-06
vg0139921470 sf0139920427 1 39921470 5.40E-09 1.04E-06
vg0601639995 sf0601638996 6 1639995 7.41E-09 2.30E-06
vg1003557200 sf1003556177 10 3557200 NA 1.69E-06