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 mr1291 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
vg0619405763 sf0619404766 6 19405763 2.66E-08 5.63E-07
vg1001340938 sf1001339915 10 1340938 1.60E-07 3.34E-06
vg0419763927 sf0419591962 4 19763927 7.12E-07 6.19E-07
vg1000028798 sf1000027798 10 28798 NA 7.93E-07
vg1214046223 sf1214043563 12 14046223 NA 9.42E-07
vg1216602681 sf1216599974 12 16602681 NA 1.50E-06
vg1213799974 sf1213797312 12 13799974 NA 2.37E-06