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 mr1797 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
vg0118124341 sf0118123295 1 18124341 1.20E-06 1.20E-06
vg0728386858 sf0728385866 7 28386858 1.54E-06 1.54E-06
vg0816052546 sf0816049832 8 16052546 2.10E-06 2.10E-06
vg0123918111 sf0123917067 1 23918111 2.22E-06 2.22E-06
vg0111972572 sf0111971546 1 11972572 2.92E-06 2.92E-06
vg0223433169 sf0223427300 2 23433169 4.57E-06 4.57E-06
vg1122373396 sf1121907267 11 22373396 4.71E-06 4.72E-06