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 mr1381 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
vg0709984451 sf0709983457 7 9984451 6.25E-09 1.51E-07
vg0431498650 sf0431313549 4 31498650 9.90E-09 4.58E-07
vg0820968372 sf0820965659 8 20968372 1.56E-08 3.85E-07
vg0820968829 sf0820966116 8 20968829 2.20E-08 3.65E-07
vg1104963383 sf1104959194 11 4963383 5.89E-08 NA
vg0725433712 sf0725432718 7 25433712 7.05E-08 NA
vg0807410855 sf0807409860 8 7410855 1.97E-07 4.05E-07
vg1105281315 sf1105277066 11 5281315 2.95E-07 2.34E-06
vg0710331865 sf0710330871 7 10331865 6.57E-07 2.20E-06
vg0327968455 sf0327961509 3 27968455 1.01E-06 2.63E-06
vg0207908595 sf0207908594 2 7908595 1.90E-06 NA
vg1219591736 sf1219563206 12 19591736 2.19E-06 3.20E-06
vg0726932825 sf0726931831 7 26932825 4.37E-06 NA
vg0304654587 sf0304653589 3 4654587 6.11E-06 NA