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 mr1366 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
vg0819540823 sf0819538110 8 19540823 1.85E-07 1.85E-07
vg0431515534 sf0431330433 4 31515534 1.99E-07 1.99E-07
vg1214822308 sf1214819649 12 14822308 6.83E-07 6.84E-07
vg0200528076 sf0200528076 2 528076 8.00E-07 8.01E-07
vg0203000556 sf0203000554 2 3000556 1.16E-06 1.15E-06
vg0132110795 sf0132109751 1 32110795 1.74E-06 1.75E-06
vg0627911377 sf0627910379 6 27911377 2.09E-06 2.10E-06
vg0128472469 sf0128471424 1 28472469 2.37E-06 2.38E-06
vg0822105767 sf0822103054 8 22105767 2.72E-06 2.69E-06
vg1214600105 sf1214597445 12 14600105 2.93E-06 2.92E-06
vg0821970212 sf0821967499 8 21970212 3.33E-06 3.28E-06
vg0922292101 sf0922291620 9 22292101 4.30E-06 4.31E-06