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 mr1362 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
vg0817608868 sf0817606155 8 17608868 1.24E-08 7.51E-07
vg0810682226 sf0810681230 8 10682226 1.71E-06 2.90E-06
vg1213459961 sf1213457299 12 13459961 NA 1.20E-07
vg1000804159 sf1000803135 10 804159 NA 8.64E-07
vg1211533655 sf1211530991 12 11533655 NA 4.17E-06
vg0727529174 sf0727528180 7 27529174 NA 6.51E-06
vg1214804175 sf1214801516 12 14804175 NA 8.35E-06