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 mr1802 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
vg1218087170 sf1218058606 12 18087170 6.80E-08 8.66E-06
vg0500972422 sf0500972405 5 972422 7.66E-08 NA
vg0711997472 sf0711996478 7 11997472 NA 2.30E-06
vg0920894235 sf0920893754 9 20894235 NA 2.72E-06
vg0706378896 sf0706377901 7 6378896 NA 3.60E-06
vg0522311777 sf0522249218 5 22311777 NA 4.24E-06