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 mr1568 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
vg0520272415 sf0520209888 5 20272415 1.09E-07 1.09E-07
vg1004374773 sf1004391311 10 4374773 4.49E-07 4.49E-07
vg0623833223 sf0623832226 6 23833223 1.83E-06 1.83E-06
vg1214592827 sf1214590167 12 14592827 1.90E-06 1.90E-06
vg0423536187 sf0423351044 4 23536187 2.59E-06 2.59E-06
vg0334515770 sf0334508640 3 34515770 3.02E-06 3.02E-06
vg0427386199 sf0427201063 4 27386199 4.05E-06 4.05E-06