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 mr1042 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
vg0226083118 sf0226077249 2 26083118 4.09E-09 2.77E-06
vg0225607950 sf0225602081 2 25607950 7.75E-09 1.89E-06
vg0223207791 sf0223201922 2 23207791 3.11E-08 NA
vg0701556427 sf0701555427 7 1556427 7.49E-08 NA
vg0420705057 sf0420533100 4 20705057 5.22E-07 4.32E-06
vg1204623407 sf1204622395 12 4623407 2.25E-06 NA
vg1208562683 sf1208560090 12 8562683 2.88E-06 4.78E-06