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 mr1020 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
vg0610871475 sf0610870476 6 10871475 8.21E-26 6.41E-06
vg0615068881 sf0615067882 6 15068881 6.60E-25 NA
vg0614107939 sf0614106940 6 14107939 1.07E-24 1.26E-07
vg0620627981 sf0620626984 6 20627981 1.13E-24 NA
vg0620812986 sf0620811989 6 20812986 3.10E-24 9.78E-07
vg0620632762 sf0620631765 6 20632762 4.85E-24 1.38E-06
vg0616691629 sf0616690631 6 16691629 8.00E-24 3.45E-06
vg0617765147 sf0617764150 6 17765147 8.47E-24 NA
vg1017458025 sf1017386798 10 17458025 9.19E-24 NA
vg0610873780 sf0610872781 6 10873780 7.87E-23 1.53E-06
vg1004618983 sf1004635521 10 4618983 NA 7.61E-09
vg0610799620 sf0610798621 6 10799620 NA 3.04E-07
vg0608916603 sf0608915604 6 8916603 NA 7.63E-07
vg1004572201 sf1004588739 10 4572201 NA 9.89E-07
vg1004560628 sf1004577166 10 4560628 NA 3.91E-06
vg1123159214 sf1122693085 11 23159214 NA 4.22E-06
vg1210252343 sf1210249755 12 10252343 NA 6.17E-06