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 mr1790 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
vg1119890467 sf1119424390 11 19890467 6.39E-08 3.28E-06
vg0514727200 sf0514669743 5 14727200 7.75E-08 2.44E-06
vg0514727249 sf0514669792 5 14727249 9.45E-08 2.57E-06
vg0300033578 sf0300032578 3 33578 2.76E-07 4.14E-06
vg1118805754 sf1118339562 11 18805754 7.89E-07 NA
vg0432283565 sf0432098457 4 32283565 1.25E-06 8.44E-06
vg0900146158 sf0900145158 9 146158 2.66E-06 1.05E-06
vg0111652887 sf0111651861 1 11652887 NA 4.91E-06