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 mr1202 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
vg0222725103 sf0222719234 2 22725103 7.71E-36 9.22E-22
vg0224233917 sf0224228048 2 24233917 7.26E-12 1.19E-07
vg0224676560 sf0224670691 2 24676560 2.20E-11 1.42E-08
vg0224293976 sf0224288107 2 24293976 1.17E-10 1.48E-07
vg0223635846 sf0223629977 2 23635846 1.23E-10 NA
vg1112606022 sf1112142225 11 12606022 1.64E-10 3.62E-06
vg0222671915 sf0222666046 2 22671915 1.10E-08 4.52E-09
vg0809948045 sf0809947049 8 9948045 2.42E-08 1.44E-06
vg0222798657 sf0222792788 2 22798657 1.13E-07 1.91E-06
vg0904658178 sf0904657178 9 4658178 6.88E-07 4.05E-07
vg0613063818 sf0613062819 6 13063818 8.46E-07 NA
vg0421072597 sf0420900652 4 21072597 9.37E-07 2.07E-06
vg0809991680 sf0809990684 8 9991680 4.31E-06 1.99E-06