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 mr1928 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
vg0727101410 sf0727100416 7 27101410 1.62E-10 1.77E-11
vg0400958004 sf0400953556 4 958004 1.92E-09 1.90E-08
vg1223982521 sf1223948974 12 23982521 1.94E-09 NA
vg0721979350 sf0721978357 7 21979350 8.41E-09 1.33E-07
vg0323673353 sf0323671527 3 23673353 9.23E-09 4.45E-06
vg0410080228 sf0410070926 4 10080228 3.25E-08 3.68E-08
vg0712655383 sf0712654390 7 12655383 5.43E-08 8.15E-07
vg0723953215 sf0723952221 7 23953215 1.66E-07 3.05E-08
vg1208322523 sf1208319929 12 8322523 2.85E-07 2.06E-07
vg0800426468 sf0800425468 8 426468 3.64E-07 NA
vg0327185700 sf0327178753 3 27185700 1.19E-06 3.28E-08
vg0902154424 sf0902153424 9 2154424 2.08E-06 1.35E-06
vg0727932446 sf0727931453 7 27932446 3.17E-06 3.50E-06
vg0208101334 sf0208101333 2 8101334 3.59E-06 4.26E-06
vg0612945611 sf0612944612 6 12945611 3.86E-06 7.23E-07
vg0711374428 sf0711373434 7 11374428 5.01E-06 3.31E-06
vg0406779682 sf0406775127 4 6779682 NA 2.77E-07
vg0228486501 sf0228480632 2 28486501 NA 4.64E-06