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 mr1222 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
vg0222725881 sf0222720012 2 22725881 2.64E-53 2.35E-40
vg0223979309 sf0223973440 2 23979309 3.56E-12 4.74E-07
vg0222879623 sf0222873754 2 22879623 9.90E-12 6.82E-11
vg0224284988 sf0224279119 2 24284988 7.33E-11 NA
vg0223641214 sf0223635345 2 23641214 1.64E-10 1.81E-08
vg0222624829 sf0222618960 2 22624829 1.26E-09 1.62E-10
vg0224664402 sf0224658533 2 24664402 1.54E-09 5.23E-09
vg0223172089 sf0223166220 2 23172089 1.71E-09 3.04E-07
vg0223820416 sf0223814547 2 23820416 2.01E-08 3.15E-06
vg0222857256 sf0222851387 2 22857256 3.47E-08 4.07E-07
vg0335727001 sf0335719870 3 35727001 4.34E-08 1.74E-06
vg0225441549 sf0225435680 2 25441549 4.87E-08 1.33E-07
vg0820681231 sf0820678518 8 20681231 4.93E-08 1.89E-06
vg1112606022 sf1112142225 11 12606022 8.41E-08 4.09E-07
vg0222041029 sf0222035160 2 22041029 4.35E-07 2.84E-06
vg0709806584 sf0709805590 7 9806584 NA 2.85E-06
vg0421189516 sf0421017568 4 21189516 NA 3.44E-06
vg0223720122 sf0223714253 2 23720122 NA 3.93E-06