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 mr1879 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
vg0717067453 sf0717066460 7 17067453 4.90E-08 7.85E-08
vg0335609544 sf0335602413 3 35609544 5.15E-08 NA
vg0619807095 sf0619806098 6 19807095 9.03E-08 NA
vg0625068802 sf0625067805 6 25068802 2.05E-06 3.80E-06
vg0405892361 sf0405887802 4 5892361 2.34E-06 3.81E-06
vg1110154705 sf1110149282 11 10154705 8.28E-06 NA