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 mr1596 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
vg0903223470 sf0903222470 9 3223470 6.45E-11 2.24E-06
vg1219410821 sf1219382291 12 19410821 1.86E-10 4.80E-06
vg0513696601 sf0513639145 5 13696601 2.74E-10 NA
vg0126439651 sf0126438607 1 26439651 9.46E-10 4.26E-07
vg0422562393 sf0422377278 4 22562393 4.81E-09 NA
vg0422542724 sf0422357611 4 22542724 1.16E-08 3.75E-06
vg1219433344 sf1219404814 12 19433344 1.14E-07 3.97E-06
vg0425061026 sf0424875887 4 25061026 1.24E-07 2.53E-06
vg0407833565 sf0407828833 4 7833565 2.12E-07 3.90E-06
vg0702624412 sf0702623413 7 2624412 2.39E-07 1.71E-06
vg1119485334 sf1119019022 11 19485334 NA 2.48E-06
vg0128560757 sf0128559712 1 28560757 NA 4.13E-06