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 mr1666 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
vg1001964474 sf1001963451 10 1964474 3.31E-07 3.31E-07
vg0819106870 sf0819104157 8 19106870 6.48E-07 6.48E-07
vg0616709270 sf0616708272 6 16709270 6.69E-07 6.69E-07
vg1121646803 sf1121180680 11 21646803 9.94E-07 9.94E-07
vg0401768023 sf0401763619 4 1768023 1.09E-06 1.09E-06
vg0321868645 sf0321867155 3 21868645 1.10E-06 1.10E-06
vg1119579044 sf1119112732 11 19579044 2.20E-06 2.20E-06
vg1112943242 sf1112479563 11 12943242 2.25E-06 2.25E-06
vg0620931744 sf0620930747 6 20931744 4.71E-06 4.71E-06