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 mr1013 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
vg0130113615 sf0130112570 1 30113615 1.53E-10 NA
vg0326411329 sf0326404423 3 26411329 6.92E-10 NA
vg1222577692 sf1222544131 12 22577692 1.13E-09 7.10E-06
vg0217651623 sf0217645753 2 17651623 1.43E-09 NA
vg0138103681 sf0138102638 1 38103681 1.93E-09 NA
vg0110154128 sf0110153104 1 10154128 6.01E-09 9.35E-06
vg1222561211 sf1222527650 12 22561211 2.80E-07 4.83E-06
vg0138140595 sf0138139552 1 38140595 3.88E-07 8.76E-06
vg0915452929 sf0915451928 9 15452929 2.55E-06 NA