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 mr1165 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 3.76E-27 1.35E-11
vg0615922178 sf0615921180 6 15922178 1.36E-22 7.04E-07
vg0205511721 sf0205511721 2 5511721 9.33E-22 NA
vg0618509091 sf0618508094 6 18509091 1.13E-21 NA
vg0614795778 sf0614794779 6 14795778 4.07E-21 4.19E-09
vg0525495929 sf0525433350 5 25495929 6.14E-21 NA
vg0617514501 sf0617513504 6 17514501 1.88E-20 3.30E-06
vg0620630387 sf0620629390 6 20630387 4.55E-20 2.83E-07
vg0610367772 sf0610366773 6 10367772 NA 3.01E-10
vg0610926231 sf0610925232 6 10926231 NA 1.28E-07
vg0610884370 sf0610883371 6 10884370 NA 1.41E-07
vg0610829284 sf0610828285 6 10829284 NA 1.50E-07
vg0611438806 sf0611437807 6 11438806 NA 1.92E-07
vg0526989730 sf0526927086 5 26989730 NA 9.49E-07
vg0610605520 sf0610604521 6 10605520 NA 1.10E-06
vg1004618983 sf1004635521 10 4618983 NA 1.20E-06
vg0610211070 sf0610210071 6 10211070 NA 4.10E-06
vg1004623300 sf1004639838 10 4623300 NA 4.26E-06
vg0610763769 sf0610762770 6 10763769 NA 9.15E-06