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 mr1950 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
vg0405539066 sf0405534507 4 5539066 1.65E-11 2.73E-08
vg0421013459 sf0420841512 4 21013459 1.60E-09 1.80E-07
vg0404471156 sf0404466760 4 4471156 1.36E-08 1.40E-06
vg0614458476 sf0614457477 6 14458476 6.62E-08 9.77E-06
vg0419885029 sf0419713065 4 19885029 9.66E-07 3.55E-06
vg0404403925 sf0404399529 4 4403925 1.30E-06 2.60E-06
vg1015203758 sf1015132526 10 15203758 3.92E-06 1.83E-07
vg0716180373 sf0716179380 7 16180373 NA 2.45E-06