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 mr1800 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
vg1018606073 sf1018534630 10 18606073 1.85E-13 3.90E-07
vg0523062907 sf0523000348 5 23062907 4.94E-12 NA
vg0106130897 sf0106129897 1 6130897 8.50E-12 NA
vg0503778745 sf0503778722 5 3778745 2.25E-11 NA
vg0217022731 sf0217016861 2 17022731 4.75E-11 NA