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 mr1141 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
vg1209876216 sf1209873626 12 9876216 1.62E-08 1.62E-08
vg1222234300 sf1222200847 12 22234300 1.45E-06 1.45E-06
vg1016814608 sf1016743380 10 16814608 1.57E-06 1.57E-06
vg0202518756 sf0202518754 2 2518756 1.67E-06 1.67E-06
vg1128773900 sf1128250679 11 28773900 1.93E-06 1.93E-06
vg0917543857 sf0917542856 9 17543857 2.54E-06 2.54E-06
vg0612661215 sf0612660216 6 12661215 2.64E-06 2.64E-06
vg0911597491 sf0911596490 9 11597491 3.10E-06 3.10E-06
vg0311072594 sf0311071312 3 11072594 3.16E-06 3.16E-06