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 mr1360 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
vg0706644677 sf0706643682 7 6644677 6.33E-08 6.33E-08
vg0330653946 sf0330646833 3 30653946 9.39E-08 9.40E-08
vg1220035763 sf1220007205 12 20035763 2.00E-06 2.00E-06
vg0707566881 sf0707565886 7 7566881 2.44E-06 2.44E-06
vg0210408970 sf0210408968 2 10408970 3.43E-06 3.43E-06
vg0206770823 sf0206770823 2 6770823 4.19E-06 4.19E-06
vg0210111974 sf0210111972 2 10111974 4.29E-06 4.29E-06
vg1126694376 sf1126222763 11 26694376 4.72E-06 4.72E-06
vg1219556752 sf1219528222 12 19556752 4.91E-06 4.91E-06
vg1218153748 sf1218125184 12 18153748 8.66E-06 8.66E-06