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 mr1384 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
vg0606378730 sf0606377731 6 6378730 3.27E-07 3.27E-07
vg0317961609 sf0317960391 3 17961609 3.92E-07 3.92E-07
vg1206182541 sf1206181432 12 6182541 8.52E-07 8.52E-07
vg0222037003 sf0222031134 2 22037003 1.21E-06 1.21E-06
vg0626850754 sf0626849757 6 26850754 2.37E-06 2.37E-06
vg0224380989 sf0224375120 2 24380989 2.37E-06 2.37E-06
vg0423711696 sf0423526553 4 23711696 2.43E-06 2.43E-06
vg0307653172 sf0307652110 3 7653172 2.83E-06 2.83E-06
vg0727277278 sf0727276284 7 27277278 2.85E-06 2.85E-06
vg0336159623 sf0336152549 3 36159623 3.17E-06 3.17E-06
vg1104966583 sf1104962394 11 4966583 4.53E-06 4.53E-06