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 mr1176 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
vg0612828976 sf0612827977 6 12828976 6.21E-11 2.93E-07
vg0613389030 sf0613388031 6 13389030 7.67E-11 2.56E-06
vg0619639208 sf0619638211 6 19639208 6.37E-10 2.31E-06
vg0617622749 sf0617621752 6 17622749 2.48E-09 5.55E-06
vg0820390658 sf0820387945 8 20390658 2.88E-09 NA
vg0216120581 sf0216114711 2 16120581 4.73E-08 6.40E-08
vg0226057933 sf0226052064 2 26057933 3.49E-07 2.54E-07
vg0516238439 sf0516180921 5 16238439 1.57E-06 1.02E-06
vg1218168989 sf1218140425 12 18168989 NA 5.75E-07
vg0623427584 sf0623426587 6 23427584 NA 6.07E-07
vg1218108461 sf1218079897 12 18108461 NA 1.49E-06
vg0804343793 sf0804342796 8 4343793 NA 4.49E-06
vg0804343386 sf0804342389 8 4343386 NA 4.64E-06