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 mr1545 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
vg0705056076 sf0705055077 7 5056076 2.78E-09 NA
vg0825106864 sf0825104150 8 25106864 5.18E-09 NA
vg0422284898 sf0422099780 4 22284898 5.58E-09 NA
vg0401725165 sf0401720714 4 1725165 5.68E-09 NA
vg0701137593 sf0701136593 7 1137593 1.19E-08 NA
vg0502169913 sf0502169888 5 2169913 1.14E-07 1.33E-06
vg0602120650 sf0602119651 6 2120650 1.43E-06 2.26E-06
vg0316680679 sf0316679324 3 16680679 1.75E-06 3.97E-06
vg1218047368 sf1218018804 12 18047368 1.82E-06 2.43E-06