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 mr1407 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
vg1214950937 sf1214948279 12 14950937 2.18E-07 2.18E-07
vg1214729813 sf1214727154 12 14729813 2.91E-07 2.91E-07
vg0405227428 sf0405222869 4 5227428 8.64E-07 8.65E-07
vg1102677343 sf1102673247 11 2677343 9.36E-07 9.37E-07
vg0921095515 sf0921095034 9 21095515 4.65E-06 4.65E-06