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 mr1062 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
vg0405591691 sf0405587132 4 5591691 2.44E-40 1.04E-22
vg0405375041 sf0405370482 4 5375041 1.69E-36 4.15E-23
vg0405735471 sf0405730910 4 5735471 1.80E-32 1.67E-20
vg0232791648 sf0232785779 2 32791648 1.92E-29 2.69E-09
vg0523114802 sf0523052243 5 23114802 8.42E-25 NA
vg0130905507 sf0130904463 1 30905507 1.55E-24 NA
vg1113797630 sf1113333951 11 13797630 5.41E-23 4.73E-09
vg0405856867 sf0405852308 4 5856867 6.99E-23 5.41E-08
vg0410659754 sf0410650454 4 10659754 1.51E-22 3.55E-09
vg0405444484 sf0405439925 4 5444484 3.28E-21 2.57E-09
vg0405316061 sf0405311502 4 5316061 2.22E-17 2.49E-08
vg0405677437 sf0405672876 4 5677437 NA 8.82E-20
vg0405440340 sf0405435781 4 5440340 NA 1.95E-10
vg0405309804 sf0405305245 4 5309804 NA 1.39E-09
vg0410128864 sf0410119561 4 10128864 NA 4.76E-09
vg0232811799 sf0232805930 2 32811799 NA 6.09E-09
vg0619746470 sf0619745473 6 19746470 NA 1.01E-08
vg0405437883 sf0405433324 4 5437883 NA 3.39E-08
vg0803241999 sf0803241002 8 3241999 NA 3.71E-08
vg0431016407 sf0430831287 4 31016407 NA 8.93E-08
vg0803430215 sf0803429218 8 3430215 NA 1.53E-07
vg0408601706 sf0408596980 4 8601706 NA 2.83E-07
vg0301474140 sf0301473138 3 1474140 NA 3.63E-07
vg0225854672 sf0225848803 2 25854672 NA 3.90E-07
vg0726548313 sf0726547319 7 26548313 NA 7.51E-07