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 mr1671 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
vg0304273109 sf0304272111 3 4273109 5.93E-93 1.02E-06
vg0627387528 sf0627386531 6 27387528 5.77E-92 NA
vg0122087924 sf0122086879 1 22087924 9.95E-91 NA
vg0334653299 sf0334646169 3 34653299 5.53E-90 NA
vg0707116055 sf0707115060 7 7116055 5.44E-89 NA
vg0334633999 sf0334626869 3 34633999 1.08E-85 3.82E-15
vg0304319579 sf0304318581 3 4319579 1.88E-78 7.81E-10
vg0334580739 sf0334573609 3 34580739 NA 3.04E-14
vg0304338025 sf0304337027 3 4338025 NA 8.09E-09
vg0726383683 sf0726382689 7 26383683 NA 1.28E-07
vg0503843762 sf0503843739 5 3843762 NA 1.39E-06
vg0324949511 sf0324947591 3 24949511 NA 1.62E-06
vg1000738859 sf1000737835 10 738859 NA 2.47E-06
vg0811071019 sf0811070024 8 11071019 NA 3.50E-06
vg0805155218 sf0805154221 8 5155218 NA 4.94E-06
vg1120296880 sf1119830804 11 20296880 NA 8.99E-06