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 mr1668 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
vg0608027015 sf0608026016 6 8027015 4.53E-12 2.26E-08
vg0607988536 sf0607987537 6 7988536 6.00E-12 4.16E-09
vg0316850166 sf0316849040 3 16850166 5.04E-08 6.72E-06
vg0504496516 sf0504496493 5 4496516 5.67E-08 NA
vg0316790922 sf0316789796 3 16790922 2.14E-06 NA
vg0521875329 sf0521812771 5 21875329 5.11E-06 NA