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 mr1652 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
vg1216110511 sf1216107807 12 16110511 1.57E-08 2.01E-07
vg1020531763 sf1020460242 10 20531763 2.81E-08 2.58E-06
vg0727503955 sf0727502961 7 27503955 3.99E-08 NA
vg0717126175 sf0717125182 7 17126175 5.84E-08 3.89E-06
vg0142427760 sf0142426716 1 42427760 6.03E-08 5.47E-06
vg0420718113 sf0420546156 4 20718113 2.54E-06 1.38E-06
vg0516508609 sf0516451091 5 16508609 6.50E-06 2.37E-06
vg0521659473 sf0521596915 5 21659473 NA 1.59E-06
vg0905437685 sf0905436685 9 5437685 NA 2.96E-06
vg0717081055 sf0717080062 7 17081055 NA 3.54E-06