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 mr1405 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
vg0713306656 sf0713305663 7 13306656 7.06E-09 NA
vg0710776650 sf0710775656 7 10776650 7.57E-09 NA
vg0918906558 sf0918905558 9 18906558 1.35E-08 NA
vg0140420434 sf0140419391 1 40420434 1.37E-08 NA
vg0433421279 sf0433236168 4 33421279 1.66E-08 7.93E-06
vg0433410224 sf0433225113 4 33410224 4.77E-08 7.26E-06
vg0810682742 sf0810681746 8 10682742 8.22E-07 3.65E-06
vg0607540736 sf0607539737 6 7540736 3.52E-06 NA
vg1119430301 sf1118963989 11 19430301 5.28E-06 NA
vg0431515534 sf0431330433 4 31515534 7.45E-06 2.95E-06