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 mr1589 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
vg0627929341 sf0627928343 6 27929341 1.41E-08 1.41E-08
vg0108533994 sf0108532994 1 8533994 6.21E-08 6.21E-08
vg0222065930 sf0222060061 2 22065930 7.27E-08 7.27E-08
vg0107544024 sf0107543024 1 7544024 7.73E-08 7.73E-08
vg1107499796 sf1107495541 11 7499796 5.21E-07 5.21E-07
vg0432505180 sf0432320072 4 32505180 6.58E-07 6.58E-07
vg0910545581 sf0910544580 9 10545581 7.05E-07 7.05E-07
vg1127121896 sf1126650283 11 27121896 7.71E-07 7.71E-07
vg0727090466 sf0727089472 7 27090466 9.80E-07 9.80E-07
vg0222531687 sf0222525818 2 22531687 1.22E-06 1.22E-06
vg1103697850 sf1103693752 11 3697850 1.85E-06 1.85E-06
vg0221025908 sf0221020040 2 21025908 2.24E-06 2.24E-06
vg0124571825 sf0124570781 1 24571825 2.67E-06 2.67E-06
vg0135058637 sf0135057594 1 35058637 2.86E-06 2.86E-06
vg1106988724 sf1106984469 11 6988724 3.34E-06 3.34E-06
vg0805855827 sf0805854830 8 5855827 3.76E-06 3.76E-06
vg0628759426 sf0628758428 6 28759426 4.11E-06 4.11E-06