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 mr1420 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
vg0721356842 sf0721355849 7 21356842 2.15E-09 NA
vg0141835472 sf0141834429 1 41835472 2.22E-09 NA
vg0902107236 sf0902106236 9 2107236 2.61E-09 3.50E-06
vg0724771358 sf0724770364 7 24771358 3.93E-09 NA
vg0915815139 sf0915814138 9 15815139 7.32E-09 NA
vg1207840077 sf1207837483 12 7840077 1.97E-07 5.99E-06
vg0304539133 sf0304538135 3 4539133 2.29E-06 NA