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 mr1396 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
vg0323080522 sf0323079010 3 23080522 2.77E-07 2.77E-07
vg1017995481 sf1017924253 10 17995481 6.94E-07 6.94E-07
vg0404503559 sf0404499163 4 4503559 7.22E-07 7.22E-07
vg0615545789 sf0615544791 6 15545789 1.35E-06 1.35E-06
vg0613801975 sf0613800976 6 13801975 1.86E-06 1.86E-06
vg1016561016 sf1016489789 10 16561016 3.25E-06 3.26E-06
vg0217328110 sf0217322240 2 17328110 4.12E-06 4.12E-06
vg1102140175 sf1102136033 11 2140175 9.08E-06 9.08E-06
vg0900126135 sf0900125135 9 126135 9.68E-06 9.68E-06