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 mr1564 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
vg0328105782 sf0328098836 3 28105782 4.44E-09 NA
vg1122514350 sf1122048221 11 22514350 3.20E-08 2.64E-07
vg0225101538 sf0225095669 2 25101538 3.35E-08 NA
vg1222927642 sf1222894101 12 22927642 3.86E-08 3.58E-06
vg0226014296 sf0226008427 2 26014296 8.47E-08 NA
vg0105137567 sf0105136567 1 5137567 5.07E-07 5.77E-06
vg0521217382 sf0521154823 5 21217382 4.14E-06 NA
vg1119340990 sf1118874678 11 19340990 NA 1.68E-06