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 mr1942 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
vg1102427853 sf1102423757 11 2427853 5.50E-09 NA
vg0143071013 sf0143069969 1 43071013 1.53E-08 NA
vg1018295419 sf1018223976 10 18295419 1.79E-08 NA
vg1123361505 sf1122895375 11 23361505 2.22E-08 NA
vg1104292362 sf1104288264 11 4292362 2.63E-08 NA
vg0828200030 sf0828197316 8 28200030 8.93E-08 1.26E-07
vg0417867500 sf0417695542 4 17867500 2.69E-06 NA
vg0817965815 sf0817963102 8 17965815 5.54E-06 6.39E-06
vg0803246961 sf0803245964 8 3246961 NA 3.64E-06