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 mr1317 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
vg0217095683 sf0217089813 2 17095683 2.54E-53 2.45E-30
vg1108225523 sf1108220133 11 8225523 2.97E-21 7.35E-06
vg1220336317 sf1220307759 12 20336317 3.95E-20 2.12E-07
vg1015182556 sf1015111324 10 15182556 1.29E-18 NA
vg0212591710 sf0212591706 2 12591710 2.68E-18 4.74E-08
vg1216728542 sf1216722496 12 16728542 1.96E-14 4.34E-07
vg0216121609 sf0216115739 2 16121609 2.65E-13 3.30E-07
vg1003674168 sf1003673145 10 3674168 8.38E-13 5.07E-08
vg0211870399 sf0211870395 2 11870399 8.64E-12 4.53E-06
vg0710676728 sf0710675734 7 10676728 9.55E-12 2.35E-06
vg0217324370 sf0217318500 2 17324370 6.74E-09 4.11E-09
vg0412260112 sf0412250827 4 12260112 7.18E-08 NA
vg0216764706 sf0216758836 2 16764706 7.21E-08 1.92E-06