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 mr1849 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
vg1122466562 sf1122000433 11 22466562 3.96E-07 3.96E-07
vg0614018205 sf0614017206 6 14018205 2.40E-06 2.41E-06
vg0319153986 sf0319152746 3 19153986 2.56E-06 2.57E-06
vg1217923635 sf1217895069 12 17923635 2.73E-06 2.73E-06
vg0827509408 sf0827506694 8 27509408 3.37E-06 3.38E-06
vg0915823657 sf0915822656 9 15823657 4.08E-06 4.07E-06