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 mr1456 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
vg0520547429 sf0520484870 5 20547429 3.71E-08 3.71E-08
vg1201238278 sf1201237278 12 1238278 6.48E-08 6.48E-08
vg0907839387 sf0907838387 9 7839387 2.54E-07 2.54E-07
vg0517184431 sf0517124072 5 17184431 2.89E-07 2.89E-07
vg1120858563 sf1120392466 11 20858563 3.30E-07 3.31E-07
vg1121965345 sf1121499216 11 21965345 6.28E-07 6.28E-07
vg0827295988 sf0827293274 8 27295988 1.38E-06 1.38E-06
vg0124233988 sf0124232944 1 24233988 1.69E-06 1.69E-06
vg1017951405 sf1017880177 10 17951405 2.01E-06 2.01E-06
vg0803222678 sf0803221681 8 3222678 2.02E-06 2.02E-06
vg0103604713 sf0103603713 1 3604713 2.11E-06 2.11E-06
vg0602338469 sf0602337470 6 2338469 2.69E-06 2.70E-06
vg1123390040 sf1122923910 11 23390040 2.98E-06 2.98E-06
vg0507146035 sf0507145977 5 7146035 3.62E-06 3.62E-06
vg0625083670 sf0625082673 6 25083670 4.13E-06 4.13E-06