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 mr1084 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
vg1219408131 sf1219379601 12 19408131 2.10E-16 NA
vg0810559229 sf0810558233 8 10559229 2.58E-16 9.17E-06
vg0207252101 sf0207252101 2 7252101 7.09E-16 NA
vg0814311518 sf0814308804 8 14311518 1.69E-15 NA
vg1200872917 sf1200871917 12 872917 8.10E-15 NA
vg0207214824 sf0207214824 2 7214824 1.16E-13 2.66E-06
vg1013533057 sf1013461827 10 13533057 1.99E-12 7.46E-06
vg1016877035 sf1016805807 10 16877035 NA 4.08E-09
vg1213935504 sf1213932842 12 13935504 NA 2.65E-06
vg0700407472 sf0700406472 7 407472 NA 3.15E-06
vg0220988854 sf0220982986 2 20988854 NA 6.46E-06
vg0136274627 sf0136273584 1 36274627 NA 7.89E-06