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 mr1644 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
vg1125837262 sf1125371181 11 25837262 3.22E-14 3.22E-14
vg0429135610 sf0428950470 4 29135610 1.47E-08 1.47E-08
vg1126217994 sf1125746408 11 26217994 4.07E-07 4.07E-07
vg1219735685 sf1219707155 12 19735685 8.07E-07 8.07E-07
vg1126443699 sf1125972112 11 26443699 9.54E-07 9.54E-07
vg0913746747 sf0913745746 9 13746747 1.09E-06 1.10E-06
vg1209876216 sf1209873626 12 9876216 1.16E-06 1.16E-06
vg0613038695 sf0613037696 6 13038695 1.20E-06 1.20E-06
vg1127189605 sf1126717992 11 27189605 1.24E-06 1.24E-06
vg0725076744 sf0725075750 7 25076744 1.76E-06 1.76E-06
vg1000374745 sf1000373745 10 374745 1.95E-06 1.95E-06
vg1000218960 sf1000217960 10 218960 2.87E-06 2.87E-06
vg0922900428 sf0922899947 9 22900428 3.18E-06 3.18E-06
vg1125876512 sf1125410431 11 25876512 3.36E-06 3.36E-06
vg0122924526 sf0122923482 1 22924526 3.95E-06 3.95E-06