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 mr1789 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
vg0122875553 sf0122874509 1 22875553 3.50E-39 8.02E-09
vg0311491162 sf0311489880 3 11491162 2.49E-38 1.36E-06
vg0311708093 sf0311706811 3 11708093 2.15E-37 1.13E-06
vg0126001839 sf0126000795 1 26001839 9.30E-37 NA
vg0409247981 sf0409243254 4 9247981 2.63E-36 2.62E-06
vg0407133877 sf0407129147 4 7133877 1.46E-35 1.09E-06
vg1016363331 sf1016292107 10 16363331 3.59E-35 7.78E-06
vg0409804831 sf0409795529 4 9804831 4.85E-35 1.91E-07
vg0818954184 sf0818951471 8 18954184 5.22E-29 1.22E-06
vg0117832704 sf0117831658 1 17832704 NA 1.24E-07
vg0824155625 sf0824152911 8 24155625 NA 1.28E-06
vg1115688831 sf1115225140 11 15688831 NA 1.36E-06
vg0711096071 sf0711095077 7 11096071 NA 1.82E-06
vg0411580078 sf0411570782 4 11580078 NA 3.34E-06
vg0921970933 sf0921970452 9 21970933 NA 4.03E-06
vg1223038204 sf1223004664 12 23038204 NA 4.27E-06
vg0702624412 sf0702623413 7 2624412 NA 4.46E-06
vg1222071730 sf1222038277 12 22071730 NA 4.80E-06
vg0907179681 sf0907178681 9 7179681 NA 4.86E-06