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 mr1087 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
vg0610606146 sf0610605147 6 10606146 6.14E-65 4.16E-44
vg0610661117 sf0610660118 6 10661117 3.58E-61 4.62E-46
vg0610566237 sf0610565238 6 10566237 3.91E-57 1.62E-44
vg0610584498 sf0610583499 6 10584498 1.49E-38 2.71E-30
vg0610461774 sf0610460775 6 10461774 1.90E-36 7.54E-32
vg0610358914 sf0610357915 6 10358914 9.55E-35 2.23E-25
vg0610458576 sf0610457577 6 10458576 3.49E-34 6.49E-27
vg0610564722 sf0610563723 6 10564722 1.47E-31 2.38E-24
vg0610874933 sf0610873934 6 10874933 4.59E-24 6.14E-10
vg0617815455 sf0617814458 6 17815455 2.63E-21 9.82E-10
vg0610380009 sf0610379010 6 10380009 1.41E-20 7.18E-17
vg0611292337 sf0611291338 6 11292337 5.94E-19 1.68E-14
vg0611081410 sf0611080411 6 11081410 9.89E-18 2.97E-12
vg0609873767 sf0609872768 6 9873767 4.17E-17 5.14E-13
vg0614110509 sf0614109510 6 14110509 5.89E-17 1.69E-08
vg0610442142 sf0610441143 6 10442142 3.35E-14 1.25E-14
vg0611556574 sf0611555575 6 11556574 1.52E-13 3.35E-09
vg0613809145 sf0613808146 6 13809145 1.88E-13 9.80E-11
vg0610211069 sf0610210070 6 10211069 7.26E-13 1.96E-11
vg0617595576 sf0617594579 6 17595576 2.84E-11 4.15E-08
vg0611636620 sf0611635621 6 11636620 3.06E-11 3.32E-13
vg0611651819 sf0611650820 6 11651819 1.06E-10 9.93E-11
vg0610608770 sf0610607771 6 10608770 1.27E-10 4.90E-10
vg0610681498 sf0610680499 6 10681498 3.13E-10 3.50E-10
vg0610127588 sf0610126589 6 10127588 2.64E-09 5.38E-15
vg0618988041 sf0618987044 6 18988041 3.13E-09 6.24E-12