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 mr1604 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
vg1219396594 sf1219368064 12 19396594 3.04E-10 NA
vg0909009783 sf0909008782 9 9009783 3.97E-10 NA
vg0722450841 sf0722449848 7 22450841 4.20E-10 NA
vg0330107231 sf0330100270 3 30107231 6.66E-10 NA
vg0914578790 sf0914577789 9 14578790 7.87E-10 NA
vg0722854356 sf0722853363 7 22854356 2.13E-09 NA
vg0314712121 sf0314710808 3 14712121 6.27E-09 1.84E-06
vg1118758859 sf1118292667 11 18758859 2.89E-08 NA
vg0312140797 sf0312139515 3 12140797 3.12E-08 NA
vg1214008434 sf1214005774 12 14008434 NA 1.10E-06
vg1114871222 sf1114407536 11 14871222 NA 1.84E-06