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 mr1480 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
vg0718105499 sf0718104506 7 18105499 9.81E-12 1.09E-08
vg0718117888 sf0718116895 7 18117888 4.57E-11 3.51E-09
vg0726837546 sf0726836552 7 26837546 9.42E-11 7.64E-07
vg0718107373 sf0718106380 7 18107373 1.49E-09 1.26E-08
vg0718107300 sf0718106307 7 18107300 1.87E-09 6.90E-09
vg0719633026 sf0719632033 7 19633026 4.71E-08 5.11E-06
vg0130423310 sf0130422266 1 30423310 4.73E-08 NA
vg0721027925 sf0721014314 7 21027925 8.91E-08 4.23E-06
vg0132045796 sf0132044752 1 32045796 1.78E-06 NA
vg0142632450 sf0142631406 1 42632450 2.76E-06 NA
vg1117363278 sf1116897130 11 17363278 6.93E-06 1.23E-06
vg0142491945 sf0142490901 1 42491945 NA 4.96E-06