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 mr1828 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
vg0805155489 sf0805154492 8 5155489 6.24E-07 6.24E-07
vg0526174493 sf0526111913 5 26174493 1.09E-06 1.09E-06
vg0525640125 sf0525577546 5 25640125 1.93E-06 1.93E-06
vg0207059780 sf0207059780 2 7059780 2.66E-06 2.66E-06
vg0907577141 sf0907576141 9 7577141 4.87E-06 4.87E-06
vg0615112996 sf0615111997 6 15112996 4.88E-06 4.88E-06
vg0403275601 sf0403271204 4 3275601 4.90E-06 4.90E-06