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 mr1818 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
vg0216789715 sf0216783845 2 16789715 2.27E-34 3.12E-22
vg1220336338 sf1220307780 12 20336338 1.29E-16 9.92E-08
vg1220336354 sf1220307796 12 20336354 1.97E-16 8.79E-08
vg1216728961 sf1216722915 12 16728961 1.38E-14 NA
vg1108225523 sf1108220133 11 8225523 3.52E-14 7.07E-06
vg0725840534 sf0725839540 7 25840534 8.70E-14 6.50E-08
vg1216728542 sf1216722496 12 16728542 2.88E-11 2.51E-07
vg1003674168 sf1003673145 10 3674168 3.30E-11 7.92E-08
vg0211870399 sf0211870395 2 11870399 5.25E-11 4.15E-07
vg1216723603 sf1216717557 12 16723603 2.42E-10 1.82E-07
vg0215426540 sf0215420670 2 15426540 1.82E-08 2.45E-06
vg0216409820 sf0216403950 2 16409820 4.62E-08 2.05E-06
vg0217324261 sf0217318391 2 17324261 6.85E-08 7.25E-08
vg1114902966 sf1114439280 11 14902966 2.94E-07 3.29E-06
vg0214372057 sf0214366187 2 14372057 1.30E-06 2.17E-06
vg1106375766 sf1106371518 11 6375766 NA 2.10E-06