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 mr1831 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
vg0819603039 sf0819600326 8 19603039 7.00E-10 1.29E-08
vg0819356506 sf0819353793 8 19356506 2.26E-09 5.63E-09
vg0819848991 sf0819846278 8 19848991 3.21E-07 3.83E-06
vg0820873126 sf0820870413 8 20873126 3.45E-07 5.80E-07
vg0819654836 sf0819652123 8 19654836 1.33E-06 2.57E-06
vg1109949998 sf1109944575 11 9949998 2.09E-06 3.30E-06
vg0621412586 sf0621411589 6 21412586 3.92E-06 3.52E-06
vg1215169176 sf1215166512 12 15169176 4.94E-06 NA