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 mr1338 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
vg0519281720 sf0519219204 5 19281720 5.63E-09 NA
vg0113600906 sf0113599880 1 13600906 1.25E-08 1.99E-07
vg0617735644 sf0617734647 6 17735644 3.28E-08 2.80E-06
vg1103096922 sf1103092825 11 3096922 4.25E-08 NA
vg0907413545 sf0907412545 9 7413545 7.10E-08 NA
vg0817768586 sf0817765873 8 17768586 1.29E-06 4.42E-06
vg0600884899 sf0600883900 6 884899 4.02E-06 NA
vg0205394361 sf0205394361 2 5394361 8.78E-06 3.48E-06