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 mr1325 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
vg0103964702 sf0103963702 1 3964702 9.56E-14 NA
vg0419202195 sf0419030231 4 19202195 1.54E-13 NA
vg0504757167 sf0504757144 5 4757167 2.59E-13 NA
vg0122728935 sf0122727891 1 22728935 2.93E-13 7.77E-06
vg0122692993 sf0122691948 1 22692993 3.09E-13 3.94E-06
vg0728915189 sf0728914197 7 28915189 3.37E-13 NA
vg1003030170 sf1003029147 10 3030170 9.64E-13 NA
vg0122725849 sf0122724805 1 22725849 1.22E-12 NA
vg0518984986 sf0518922470 5 18984986 NA 2.54E-06
vg1214701611 sf1214698952 12 14701611 NA 4.56E-06