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 mr1005 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
vg0603087533 sf0603086534 6 3087533 1.69E-13 NA
vg0702311142 sf0702310143 7 2311142 6.01E-13 NA
vg1013330987 sf1013259756 10 13330987 1.15E-12 3.66E-06
vg0211510634 sf0211510630 2 11510634 3.26E-12 1.01E-06
vg0133257075 sf0133256031 1 33257075 7.03E-12 NA
vg1216352950 sf1216350246 12 16352950 1.01E-11 1.06E-07
vg1216156465 sf1216153761 12 16156465 1.41E-11 1.93E-06
vg0822806279 sf0822803566 8 22806279 5.99E-11 NA
vg0816652216 sf0816649502 8 16652216 NA 1.74E-07
vg0215099748 sf0215093878 2 15099748 NA 4.25E-07
vg0421477325 sf0421305376 4 21477325 NA 7.96E-07
vg1214358313 sf1214355653 12 14358313 NA 1.24E-06
vg0800803378 sf0800802380 8 803378 NA 1.83E-06
vg1016945482 sf1016874254 10 16945482 NA 2.42E-06
vg0314683652 sf0314682339 3 14683652 NA 2.44E-06
vg1224168671 sf1224135125 12 24168671 NA 3.02E-06
vg0503822720 sf0503822697 5 3822720 NA 3.51E-06
vg0602958934 sf0602957935 6 2958934 NA 3.59E-06
vg1109603153 sf1109597730 11 9603153 NA 4.17E-06