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 mr1350 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
vg0216828183 sf0216822313 2 16828183 2.57E-13 2.70E-09
vg0217010230 sf0217004360 2 17010230 2.43E-12 6.78E-10
vg0217023585 sf0217017715 2 17023585 2.55E-12 7.81E-10
vg1209191270 sf1209188679 12 9191270 1.35E-10 1.62E-08
vg0216792115 sf0216786245 2 16792115 3.33E-09 1.14E-06
vg0216347691 sf0216341821 2 16347691 2.01E-08 5.26E-07
vg1211958185 sf1211955520 12 11958185 4.12E-08 3.27E-07
vg1216728475 sf1216722429 12 16728475 5.22E-08 4.23E-06
vg0315247417 sf0315246064 3 15247417 3.32E-07 4.27E-06
vg0906569206 sf0906568206 9 6569206 4.94E-07 1.08E-06
vg1207556909 sf1207554314 12 7556909 8.77E-07 2.93E-06