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 mr1119 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
vg1008520987 sf1008449849 10 8520987 2.55E-12 2.41E-08
vg0501780624 sf0501780607 5 1780624 7.24E-11 3.56E-07
vg0407825687 sf0407820955 4 7825687 4.20E-10 6.86E-06
vg0407825479 sf0407820747 4 7825479 5.61E-10 3.64E-06
vg0502152922 sf0502152897 5 2152922 7.31E-10 8.79E-07
vg1005798437 sf1005814975 10 5798437 9.28E-10 4.91E-06
vg0614842115 sf0614841116 6 14842115 9.28E-10 2.07E-06
vg1005877950 sf1005894488 10 5877950 1.27E-09 1.78E-06
vg0528707079 sf0528644434 5 28707079 8.50E-09 2.88E-06
vg0909705729 sf0909704728 9 9705729 1.21E-07 6.38E-07
vg0912597369 sf0912596368 9 12597369 3.34E-07 3.96E-06
vg0711420958 sf0711419964 7 11420958 7.81E-07 2.11E-07
vg0516159633 sf0516102117 5 16159633 9.72E-07 2.07E-06
vg1007140460 sf1007156083 10 7140460 2.27E-06 4.27E-06
vg0316601740 sf0316600385 3 16601740 3.61E-06 3.85E-06
vg0312470741 sf0312469459 3 12470741 NA 1.74E-06
vg0729682097 sf0729681105 7 29682097 NA 4.69E-06