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 mr1726 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
vg0405539066 sf0405534507 4 5539066 1.90E-09 8.10E-06
vg1122057994 sf1121591865 11 22057994 1.63E-08 NA
vg0404444524 sf0404440128 4 4444524 2.68E-08 NA
vg0209208489 sf0209208487 2 9208489 4.40E-08 8.64E-07
vg0700314178 sf0700313178 7 314178 7.12E-08 NA
vg0404270383 sf0404265990 4 4270383 5.58E-07 5.43E-07
vg0900901867 sf0900900867 9 901867 2.52E-06 3.52E-06
vg0112163580 sf0112162554 1 12163580 2.73E-06 NA
vg0816363117 sf0816360403 8 16363117 3.21E-06 NA
vg0414582739 sf0414573453 4 14582739 3.67E-06 NA