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 mr1427 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
vg1002941211 sf1002940188 10 2941211 6.14E-09 3.08E-08
vg0910768444 sf0910767443 9 10768444 4.21E-08 5.17E-07
vg0131152445 sf0131151401 1 31152445 4.79E-07 4.68E-06
vg0139875180 sf0139874137 1 39875180 2.38E-06 4.56E-06
vg0112115913 sf0112114887 1 12115913 6.16E-06 NA
vg0132161653 sf0132160609 1 32161653 NA 4.64E-07
vg0321406609 sf0321405119 3 21406609 NA 5.66E-07