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 mr1903 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
vg0524690212 sf0524627632 5 24690212 4.79E-39 1.57E-25
vg1100184405 sf1100183406 11 184405 1.68E-17 NA
vg0524354930 sf0524292351 5 24354930 1.41E-13 NA
vg1122447036 sf1121980907 11 22447036 3.67E-13 7.94E-07
vg1200003632 sf1200002632 12 3632 6.33E-13 NA
vg0524106953 sf0524044372 5 24106953 NA 5.91E-08
vg0525881431 sf0525818852 5 25881431 NA 3.41E-06
vg0528165022 sf0528102377 5 28165022 NA 4.29E-06