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 mr1712 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
vg0306499925 sf0306498925 3 6499925 7.38E-12 NA
vg1119340990 sf1118874678 11 19340990 5.92E-11 1.53E-06
vg0602313316 sf0602312317 6 2313316 1.87E-10 NA
vg0141570346 sf0141569303 1 41570346 5.00E-10 4.32E-06
vg0309107671 sf0309106607 3 9107671 1.74E-09 NA
vg0706085714 sf0706084715 7 6085714 1.64E-07 NA
vg0308150228 sf0308149166 3 8150228 2.87E-06 1.86E-06
vg0224278447 sf0224272578 2 24278447 4.29E-06 NA
vg0817111260 sf0817108546 8 17111260 NA 2.85E-06
vg0612783393 sf0612782394 6 12783393 NA 3.14E-06
vg0909534950 sf0909533949 9 9534950 NA 3.81E-06