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 mr1664 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
vg0231417061 sf0231411192 2 31417061 6.64E-07 6.64E-07
vg0234336153 sf0234330284 2 34336153 9.00E-07 9.00E-07
vg0334841623 sf0334834493 3 34841623 1.68E-06 1.68E-06
vg0714475265 sf0714474272 7 14475265 2.08E-06 2.08E-06
vg0804453676 sf0804452679 8 4453676 2.14E-06 2.14E-06
vg0326900441 sf0326893494 3 26900441 3.63E-06 3.63E-06
vg0413845447 sf0413836165 4 13845447 4.79E-06 4.79E-06
vg0804449148 sf0804448151 8 4449148 6.40E-06 6.40E-06
vg0721100662 sf0721099669 7 21100662 6.65E-06 6.65E-06