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 mr1788 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
vg0726931180 sf0726930186 7 26931180 8.80E-09 5.27E-06
vg1210140813 sf1210138224 12 10140813 2.75E-08 NA
vg0500152728 sf0500152728 5 152728 2.84E-08 7.08E-06
vg1215165691 sf1215163027 12 15165691 5.89E-08 NA
vg0721299763 sf0721298770 7 21299763 6.72E-08 NA
vg0500084080 sf0500084080 5 84080 1.16E-07 NA
vg0710331865 sf0710330871 7 10331865 3.92E-07 2.23E-07
vg0710369624 sf0710368630 7 10369624 8.50E-07 4.42E-06
vg0620397747 sf0620396750 6 20397747 NA 1.54E-06
vg0122081051 sf0122080006 1 22081051 NA 2.37E-06
vg0511023890 sf0511023819 5 11023890 NA 3.71E-06