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 mr1824 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
vg1217948662 sf1217920096 12 17948662 3.26E-07 3.26E-07
vg0917112968 sf0917111967 9 17112968 1.27E-06 1.27E-06
vg1226901534 sf1226867933 12 26901534 1.42E-06 1.42E-06
vg0230104156 sf0230098287 2 30104156 1.52E-06 1.52E-06
vg0403780190 sf0403775795 4 3780190 1.77E-06 1.77E-06
vg0116674582 sf0116673556 1 16674582 2.49E-06 2.49E-06
vg0207218977 sf0207218977 2 7218977 2.80E-06 2.80E-06
vg1009197731 sf1009126552 10 9197731 3.03E-06 3.03E-06
vg0134670870 sf0134669827 1 34670870 3.05E-06 3.05E-06
vg0728386858 sf0728385866 7 28386858 3.16E-06 3.16E-06
vg0304592320 sf0304591322 3 4592320 3.69E-06 3.69E-06
vg0524151079 sf0524088498 5 24151079 4.22E-06 4.23E-06
vg0123918111 sf0123917067 1 23918111 4.31E-06 4.32E-06