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 mr1319 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
vg0137614990 sf0137613947 1 37614990 8.41E-17 NA
vg0104339492 sf0104338492 1 4339492 1.82E-16 NA
vg0134815001 sf0134813958 1 34815001 1.73E-15 NA
vg0131819741 sf0131818697 1 31819741 1.84E-15 NA
vg0141746853 sf0141745810 1 41746853 1.75E-13 NA
vg0703513650 sf0703512651 7 3513650 2.32E-12 3.03E-06
vg0314702972 sf0314701659 3 14702972 7.85E-10 2.30E-07
vg0704005849 sf0704004850 7 4005849 NA 3.81E-07
vg0101085958 sf0101084958 1 1085958 NA 8.78E-07
vg0109580054 sf0109579030 1 9580054 NA 8.82E-07
vg0501121695 sf0501121679 5 1121695 NA 4.16E-06