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 mr1696 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
vg0321376438 sf0321374948 3 21376438 3.06E-12 5.57E-06
vg0821929781 sf0821927068 8 21929781 8.41E-11 NA
vg1002756136 sf1002755113 10 2756136 1.38E-10 NA
vg1216595642 sf1216592935 12 16595642 1.88E-10 NA
vg0218843921 sf0218838052 2 18843921 3.23E-10 NA
vg0728490686 sf0728489694 7 28490686 1.27E-09 4.29E-06
vg0128850364 sf0128849319 1 28850364 9.07E-09 1.07E-06