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 mr1530 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
vg1125419173 sf1124953012 11 25419173 3.82E-15 1.24E-09
vg0140468617 sf0140467574 1 40468617 3.66E-14 2.02E-06
vg0430673467 sf0430488342 4 30673467 3.97E-14 5.50E-06
vg0140415588 sf0140414545 1 40415588 5.49E-14 2.03E-06
vg0140469120 sf0140468077 1 40469120 6.46E-14 1.43E-06
vg0310812131 sf0310810849 3 10812131 1.18E-13 NA
vg0204029963 sf0204029960 2 4029963 1.24E-13 NA
vg0430813005 sf0430627882 4 30813005 2.16E-11 2.72E-06
vg0507579091 sf0507579032 5 7579091 1.62E-10 5.39E-08
vg1125483609 sf1125017448 11 25483609 NA 1.39E-06