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 mr1621 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
vg0815721034 sf0815718320 8 15721034 1.73E-07 1.73E-07
vg0304467395 sf0304466397 3 4467395 2.39E-07 2.39E-07
vg0414371844 sf0414362557 4 14371844 3.39E-07 3.39E-07
vg0118939890 sf0118938845 1 18939890 6.90E-07 6.90E-07
vg0140513804 sf0140512761 1 40513804 1.61E-06 1.61E-06
vg0604502626 sf0604501627 6 4502626 2.56E-06 2.57E-06
vg1000344144 sf1000343144 10 344144 2.93E-06 2.93E-06
vg0225261737 sf0225255868 2 25261737 4.08E-06 4.08E-06
vg1218207811 sf1218179247 12 18207811 4.13E-06 4.13E-06
vg0913244556 sf0913243555 9 13244556 4.67E-06 4.67E-06