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 mr1880 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
vg0406062876 sf0406058315 4 6062876 4.39E-11 1.72E-06
vg0823044673 sf0823041960 8 23044673 1.32E-10 1.76E-06
vg0715799303 sf0715798310 7 15799303 3.96E-10 NA
vg0419769897 sf0419597932 4 19769897 4.10E-10 NA
vg0527299171 sf0527236527 5 27299171 6.11E-10 7.15E-06
vg0718994175 sf0718993182 7 18994175 1.79E-09 2.33E-07
vg0617687728 sf0617686731 6 17687728 6.77E-08 NA
vg0411129111 sf0411119812 4 11129111 1.14E-07 9.16E-07
vg0801276119 sf0801275121 8 1276119 1.99E-06 NA
vg1218068686 sf1218040122 12 18068686 2.55E-06 NA
vg0301440928 sf0301439926 3 1440928 NA 4.76E-06