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 mr1667 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
vg1125463766 sf1124997605 11 25463766 4.74E-23 3.01E-13
vg0713261979 sf0713260986 7 13261979 6.11E-19 1.07E-08
vg0604585933 sf0604584934 6 4585933 9.41E-15 NA
vg0722586628 sf0722585635 7 22586628 1.18E-14 NA
vg1020599180 sf1020527659 10 20599180 3.45E-14 NA
vg1125609790 sf1125143629 11 25609790 8.17E-14 2.33E-06
vg1125876443 sf1125410362 11 25876443 1.68E-13 3.28E-07
vg1020215571 sf1020144051 10 20215571 1.74E-13 2.50E-06
vg0722912066 sf0722911073 7 22912066 2.58E-13 9.35E-07
vg0618517700 sf0618516703 6 18517700 4.13E-13 1.78E-06
vg0607847376 sf0607846377 6 7847376 9.59E-13 3.27E-06
vg1125524321 sf1125058160 11 25524321 1.06E-11 4.34E-06
vg0619281480 sf0619280483 6 19281480 NA 3.41E-07
vg0919588048 sf0919587638 9 19588048 NA 6.71E-07
vg1127730356 sf1127258742 11 27730356 NA 6.72E-07
vg1127186610 sf1126714997 11 27186610 NA 7.44E-07
vg0619194263 sf0619193266 6 19194263 NA 8.74E-07
vg0400960642 sf0400956194 4 960642 NA 1.02E-06
vg1126298122 sf1125826535 11 26298122 NA 2.23E-06
vg0316335916 sf0316334563 3 16335916 NA 4.71E-06