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 mr1201 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
vg0622629240 sf0622628243 6 22629240 4.59E-08 2.49E-07
vg1222664248 sf1222630687 12 22664248 8.25E-08 4.51E-07
vg1216455900 sf1216453193 12 16455900 1.64E-07 4.39E-07
vg0803345287 sf0803344290 8 3345287 3.25E-07 3.11E-06
vg0602444850 sf0602443851 6 2444850 6.40E-07 2.93E-06
vg0122013494 sf0122012449 1 22013494 2.35E-06 3.20E-07
vg0319746180 sf0319744691 3 19746180 7.12E-06 4.98E-06
vg1216422905 sf1216420198 12 16422905 NA 2.13E-06
vg0104825126 sf0104824126 1 4825126 NA 4.19E-06