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 mr1543 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
vg0221812870 sf0221807001 2 21812870 1.38E-11 1.07E-09
vg1117798854 sf1117332710 11 17798854 2.97E-11 NA
vg0141963923 sf0141962880 1 41963923 7.67E-11 NA
vg1107584788 sf1107580533 11 7584788 7.35E-10 1.48E-06
vg1002880362 sf1002879339 10 2880362 7.75E-10 NA
vg1119579328 sf1119113016 11 19579328 2.70E-09 4.66E-07
vg1115275633 sf1114811947 11 15275633 3.27E-09 2.57E-07
vg0212037119 sf0212037115 2 12037119 5.70E-09 2.58E-06
vg0221875581 sf0221869712 2 21875581 1.55E-08 8.47E-07
vg0914433559 sf0914432558 9 14433559 8.58E-08 4.34E-06
vg0124891937 sf0124890893 1 24891937 6.63E-06 1.41E-06
vg0417760655 sf0417588692 4 17760655 8.83E-06 4.77E-06
vg1107500708 sf1107496453 11 7500708 NA 5.00E-07
vg0407118586 sf0407113856 4 7118586 NA 1.54E-06
vg0221847467 sf0221841598 2 21847467 NA 1.63E-06
vg0323186777 sf0323185265 3 23186777 NA 2.28E-06
vg0230955359 sf0230949490 2 30955359 NA 3.28E-06