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 mr1166 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
vg0325710457 sf0325708475 3 25710457 8.11E-10 8.11E-10
vg1005271470 sf1005288007 10 5271470 2.20E-07 2.20E-07
vg0400345487 sf0400344487 4 345487 3.16E-07 3.16E-07
vg1011018004 sf1010946824 10 11018004 9.00E-07 9.00E-07
vg0627991730 sf0627990732 6 27991730 1.00E-06 1.00E-06
vg0202817095 sf0202817093 2 2817095 1.03E-06 1.03E-06
vg1007919865 sf1007935475 10 7919865 1.83E-06 1.83E-06
vg0400034660 sf0400033660 4 34660 1.97E-06 1.97E-06
vg0209228990 sf0209228988 2 9228990 2.70E-06 2.70E-06
vg1004789770 sf1004806307 10 4789770 3.43E-06 3.43E-06
vg0429950476 sf0429765343 4 29950476 4.67E-06 4.67E-06