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 mr1457 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
vg1218590374 sf1218561810 12 18590374 4.12E-14 2.71E-09
vg1218589977 sf1218561413 12 18589977 6.93E-14 2.15E-09
vg1218593113 sf1218564549 12 18593113 1.30E-13 2.41E-09
vg1218907337 sf1218878772 12 18907337 3.48E-12 1.64E-06
vg0727982897 sf0727981904 7 27982897 5.98E-12 1.07E-10
vg0225213576 sf0225207707 2 25213576 6.94E-11 3.99E-06
vg0225214584 sf0225208715 2 25214584 2.56E-10 2.03E-06
vg0607796859 sf0607795860 6 7796859 4.90E-09 NA
vg0917927669 sf0917926668 9 17927669 1.10E-07 NA
vg1117164056 sf1116697908 11 17164056 1.32E-06 2.01E-06
vg1100016479 sf1100015479 11 16479 2.51E-06 1.98E-06