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 mr1398 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
vg0113513085 sf0113512059 1 13513085 1.13E-08 1.13E-08
vg0113491737 sf0113490711 1 13491737 1.82E-08 1.82E-08
vg0630078359 sf0630077361 6 30078359 1.99E-07 1.99E-07
vg0702566842 sf0702565843 7 2566842 7.23E-07 7.24E-07
vg0431530955 sf0431345854 4 31530955 1.21E-06 1.21E-06
vg0208482222 sf0208482221 2 8482222 2.57E-06 2.57E-06
vg0401652221 sf0401647770 4 1652221 3.45E-06 3.45E-06
vg0714713139 sf0714712146 7 14713139 3.78E-06 3.78E-06