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 mr1805 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
vg0128276891 sf0128275847 1 28276891 3.42E-32 8.06E-08
vg1224007541 sf1223973994 12 24007541 8.79E-32 7.23E-07
vg1209571189 sf1209568598 12 9571189 5.51E-31 NA
vg1209896387 sf1209893797 12 9896387 8.32E-31 1.30E-06
vg1215988665 sf1215985961 12 15988665 8.33E-31 NA
vg0216502472 sf0216496602 2 16502472 8.04E-29 NA
vg0407118586 sf0407113856 4 7118586 3.16E-25 1.85E-06
vg0820029176 sf0820026463 8 20029176 1.12E-24 8.93E-06
vg0619888183 sf0619887186 6 19888183 1.07E-23 2.34E-06
vg1011360991 sf1011289811 10 11360991 NA 5.42E-07
vg0401349008 sf0401344558 4 1349008 NA 8.16E-06