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 mr1066 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
vg0622820572 sf0622819575 6 22820572 6.78E-10 3.44E-07
vg1222498491 sf1222454852 12 22498491 1.41E-08 1.78E-06
vg0300233526 sf0300232526 3 233526 1.41E-08 NA
vg0414059978 sf0414050693 4 14059978 2.20E-08 NA
vg0727630420 sf0727629426 7 27630420 2.20E-08 NA
vg0414209097 sf0414199813 4 14209097 1.85E-07 NA
vg0226575975 sf0226570106 2 26575975 1.30E-06 1.86E-06
vg0707853841 sf0707852846 7 7853841 1.73E-06 1.31E-06
vg0622937195 sf0622936198 6 22937195 8.85E-06 4.19E-06