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 mr1869 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
vg1117178010 sf1116711862 11 17178010 1.44E-07 1.44E-07
vg1117141737 sf1116675589 11 17141737 2.54E-07 2.54E-07
vg0909816527 sf0909815526 9 9816527 5.22E-07 5.22E-07
vg0220988854 sf0220982986 2 20988854 1.25E-06 1.25E-06
vg0812018246 sf0812017251 8 12018246 3.01E-06 3.01E-06
vg0407000775 sf0406996046 4 7000775 3.86E-06 3.86E-06
vg0224823901 sf0224818032 2 24823901 4.70E-06 4.70E-06
vg1208774960 sf1208772367 12 8774960 6.16E-06 6.16E-06