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 mr1794 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
vg1009147766 sf1009076627 10 9147766 4.27E-38 5.64E-12
vg1009133110 sf1009061971 10 9133110 7.30E-38 1.50E-12
vg1006486213 sf1006501836 10 6486213 7.01E-31 5.51E-08
vg1207825767 sf1207823173 12 7825767 4.10E-27 NA
vg1008310948 sf1008239810 10 8310948 1.14E-25 9.45E-11
vg0125649810 sf0125648766 1 25649810 2.64E-25 NA
vg0134230502 sf0134229459 1 34230502 4.77E-25 NA
vg1006275887 sf1006291510 10 6275887 1.18E-24 4.13E-07
vg1202107576 sf1202106574 12 2107576 2.92E-23 2.69E-06
vg1009170287 sf1009099108 10 9170287 5.55E-23 4.58E-11
vg0407822256 sf0407817524 4 7822256 1.26E-22 2.85E-06
vg1005711741 sf1005728279 10 5711741 2.95E-19 1.93E-06
vg0500865648 sf0500865630 5 865648 6.88E-16 1.91E-06
vg0222739831 sf0222733962 2 22739831 NA 8.60E-08
vg1007509788 sf1007525411 10 7509788 NA 1.70E-07
vg0107090989 sf0107089989 1 7090989 NA 1.10E-06
vg0525591460 sf0525528881 5 25591460 NA 1.52E-06
vg0107089778 sf0107088778 1 7089778 NA 3.18E-06
vg0506611180 sf0506611121 5 6611180 NA 4.11E-06
vg1128863835 sf1128340614 11 28863835 NA 4.85E-06
vg1128865551 sf1128342330 11 28865551 NA 8.57E-06
vg0517977400 sf0517916886 5 17977400 NA 9.69E-06