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 mr1697 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
vg0223525077 sf0223519208 2 23525077 8.96E-07 8.96E-07
vg1208774850 sf1208772257 12 8774850 1.79E-06 1.78E-06
vg0209088883 sf0209088881 2 9088883 2.66E-06 2.65E-06
vg0500918476 sf0500918459 5 918476 3.14E-06 3.14E-06
vg0726559137 sf0726558143 7 26559137 3.35E-06 3.36E-06
vg0403204105 sf0403199708 4 3204105 5.03E-06 5.02E-06