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 mr1078 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
vg0610723836 sf0610722837 6 10723836 3.44E-12 6.99E-11
vg0614107939 sf0614106940 6 14107939 2.49E-09 1.27E-09
vg0202518756 sf0202518754 2 2518756 9.22E-08 4.69E-08
vg0610383233 sf0610382234 6 10383233 1.15E-07 1.17E-06
vg1222295817 sf1222262364 12 22295817 6.17E-07 9.83E-08
vg0610774978 sf0610773979 6 10774978 9.46E-07 7.41E-07
vg1222234300 sf1222200847 12 22234300 1.54E-06 1.91E-07
vg0122207812 sf0122206767 1 22207812 2.50E-06 2.16E-06
vg0707884515 sf0707883520 7 7884515 NA 2.30E-06
vg0911597491 sf0911596490 9 11597491 NA 2.87E-06