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 mr1441 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
vg0432673364 sf0432488253 4 32673364 7.46E-09 NA
vg0725366664 sf0725365670 7 25366664 8.86E-09 NA
vg0722226606 sf0722225613 7 22226606 1.22E-08 NA
vg0402093212 sf0402088806 4 2093212 1.44E-08 NA
vg0137066973 sf0137065930 1 37066973 2.07E-08 NA
vg1226987977 sf1226954376 12 26987977 1.48E-06 NA
vg0306131419 sf0306130419 3 6131419 2.90E-06 NA
vg1215569613 sf1215566910 12 15569613 4.15E-06 NA
vg1127529196 sf1127057583 11 27529196 9.45E-06 NA