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 mr1097 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
vg0130805560 sf0130804516 1 30805560 2.22E-09 5.94E-08
vg0208607058 sf0208607057 2 8607058 2.49E-09 6.81E-07
vg0130500745 sf0130499701 1 30500745 1.34E-08 1.80E-08
vg0609181739 sf0609180740 6 9181739 1.94E-08 5.50E-06
vg1115479401 sf1115015714 11 15479401 2.07E-08 3.77E-06
vg1115489572 sf1115025885 11 15489572 2.20E-08 3.32E-06
vg1110925673 sf1110919990 11 10925673 4.31E-08 NA
vg1015419562 sf1015348330 10 15419562 3.57E-06 1.81E-06
vg0131720791 sf0131719747 1 31720791 NA 2.84E-06