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 mr1657 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
vg1103068554 sf1103064458 11 3068554 2.54E-08 2.09E-07
vg0421366980 sf0421195033 4 21366980 7.34E-08 9.68E-07
vg0819985304 sf0819982591 8 19985304 1.17E-07 1.61E-06
vg0805826839 sf0805825842 8 5826839 6.44E-07 1.50E-06
vg0709448532 sf0709447538 7 9448532 7.84E-07 2.06E-06
vg0709147678 sf0709146684 7 9147678 9.97E-07 1.67E-06
vg0203208881 sf0203208879 2 3208881 3.14E-06 3.01E-06
vg0516563624 sf0516506106 5 16563624 3.44E-06 1.50E-06