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 mr1605 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
vg1213074936 sf1213072275 12 13074936 5.83E-08 5.83E-08
vg0328103960 sf0328097014 3 28103960 9.93E-07 9.93E-07
vg0506600358 sf0506600299 5 6600358 1.56E-06 1.56E-06
vg0328864309 sf0328857362 3 28864309 1.74E-06 1.74E-06
vg1127125428 sf1126653815 11 27125428 3.81E-06 3.81E-06
vg0510158281 sf0510158210 5 10158281 8.06E-06 8.06E-06