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 mr1509 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
vg0222729824 sf0222723955 2 22729824 2.92E-09 1.24E-06
vg0224678780 sf0224672911 2 24678780 9.60E-08 NA
vg0818406495 sf0818403782 8 18406495 1.81E-07 4.18E-06
vg0722613858 sf0722612865 7 22613858 3.47E-07 3.28E-06
vg0122345272 sf0122344227 1 22345272 2.61E-06 3.36E-06
vg0710533540 sf0710532546 7 10533540 4.79E-06 3.52E-06