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 mr1928 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
vg0328580055 sf0328573108 3 28580055 1.30E-09 NA
vg0500562669 sf0500562669 5 562669 2.20E-09 NA
vg0324825826 sf0324823905 3 24825826 4.26E-09 NA
vg0321123982 sf0321122492 3 21123982 6.38E-09 NA
vg0423537134 sf0423351991 4 23537134 8.00E-09 NA
vg0908550860 sf0908549859 9 8550860 4.54E-08 2.03E-06
vg0333024966 sf0333017836 3 33024966 4.89E-07 4.30E-06
vg1203462183 sf1203461183 12 3462183 1.25E-06 4.50E-06
vg0208101334 sf0208101333 2 8101334 4.91E-06 8.70E-07
vg1126919326 sf1126447713 11 26919326 6.31E-06 3.99E-06
vg0804341109 sf0804340112 8 4341109 NA 2.15E-08
vg0327185700 sf0327178753 3 27185700 NA 2.95E-07
vg0723951270 sf0723950276 7 23951270 NA 3.59E-07
vg0107287429 sf0107286429 1 7287429 NA 1.04E-06
vg1220799021 sf1220765570 12 20799021 NA 1.24E-06
vg0400791794 sf0400790794 4 791794 NA 2.38E-06
vg0902154424 sf0902153424 9 2154424 NA 3.62E-06
vg0420371360 sf0420199404 4 20371360 NA 4.47E-06
vg1002319935 sf1002318912 10 2319935 NA 4.82E-06