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 mr1450 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
vg1215653812 sf1215651109 12 15653812 6.38E-07 6.38E-07
vg0501390670 sf0501390654 5 1390670 8.17E-07 8.18E-07
vg0140479397 sf0140478354 1 40479397 1.32E-06 1.32E-06
vg0133381143 sf0133380099 1 33381143 3.50E-06 3.50E-06
vg0235058313 sf0235052444 2 35058313 3.89E-06 3.89E-06
vg1215172595 sf1215169931 12 15172595 3.90E-06 3.90E-06
vg0908028327 sf0908027327 9 8028327 4.09E-06 4.09E-06
vg0519670973 sf0519608457 5 19670973 4.22E-06 4.22E-06