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 mr1294 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
vg0220457124 sf0220451256 2 20457124 8.29E-07 8.29E-07
vg0220319668 sf0220313800 2 20319668 1.06E-06 1.06E-06
vg0918774898 sf0918773898 9 18774898 2.37E-06 2.37E-06
vg0305129097 sf0305128099 3 5129097 3.33E-06 3.33E-06
vg0805108529 sf0805107532 8 5108529 3.59E-06 3.59E-06
vg1214703763 sf1214701104 12 14703763 4.33E-06 4.33E-06
vg0314968998 sf0314967645 3 14968998 4.59E-06 4.59E-06
vg0303331756 sf0303330752 3 3331756 6.64E-06 6.64E-06