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 mr1186 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
vg0123708079 sf0123707035 1 23708079 2.44E-09 NA
vg0728156014 sf0728155021 7 28156014 5.34E-09 NA
vg0725485552 sf0725484558 7 25485552 2.03E-08 NA
vg0709448532 sf0709447538 7 9448532 2.43E-08 1.05E-06
vg0412479443 sf0412470158 4 12479443 5.96E-08 7.41E-08
vg0704732672 sf0704731673 7 4732672 1.46E-07 3.40E-06
vg0712843936 sf0712842943 7 12843936 1.68E-07 2.82E-06
vg0403204105 sf0403199708 4 3204105 2.34E-07 1.41E-07
vg0700638475 sf0700637475 7 638475 3.39E-06 NA