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 mr1030 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
vg0113283794 sf0113282768 1 13283794 2.57E-12 1.85E-06
vg0112932528 sf0112931502 1 12932528 4.38E-12 1.84E-06
vg0608096553 sf0608095554 6 8096553 1.90E-11 4.71E-06
vg0501941761 sf0501941743 5 1941761 2.38E-11 2.07E-06
vg1210574208 sf1210571621 12 10574208 2.51E-11 NA
vg0232755756 sf0232749887 2 32755756 2.51E-11 2.06E-12
vg0608081695 sf0608080696 6 8081695 3.03E-09 NA
vg0327968455 sf0327961509 3 27968455 1.30E-07 2.70E-06
vg0122195607 sf0122194562 1 22195607 2.07E-07 3.95E-06
vg0501810272 sf0501810255 5 1810272 2.10E-07 6.89E-07
vg0421020772 sf0420848825 4 21020772 NA 1.10E-06
vg0501779956 sf0501779939 5 1779956 NA 1.38E-06
vg0817557507 sf0817554793 8 17557507 NA 2.36E-06
vg0527284387 sf0527221743 5 27284387 NA 3.16E-06
vg0608145993 sf0608144994 6 8145993 NA 3.32E-06
vg1108255008 sf1108249618 11 8255008 NA 4.95E-06
vg0905400732 sf0905399732 9 5400732 NA 7.69E-06