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 mr1868 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
vg0222833455 sf0222827586 2 22833455 2.17E-09 2.17E-09
vg0220849802 sf0220843934 2 20849802 3.43E-07 3.44E-07
vg0727090466 sf0727089472 7 27090466 7.64E-07 7.63E-07
vg0627929341 sf0627928343 6 27929341 1.43E-06 1.43E-06
vg0221753297 sf0221747428 2 21753297 1.61E-06 1.61E-06
vg1003861056 sf1003860032 10 3861056 1.61E-06 1.61E-06
vg0709675216 sf0709674222 7 9675216 2.02E-06 2.02E-06
vg0428087648 sf0427902514 4 28087648 2.69E-06 2.69E-06
vg0910545581 sf0910544580 9 10545581 3.01E-06 3.01E-06
vg0628741924 sf0628740926 6 28741924 3.13E-06 3.13E-06
vg0108533994 sf0108532994 1 8533994 3.71E-06 3.71E-06
vg0221013727 sf0221007859 2 21013727 3.77E-06 3.77E-06
vg0625603773 sf0625602776 6 25603773 4.59E-06 4.59E-06
vg0432188448 sf0432003340 4 32188448 4.60E-06 4.60E-06
vg0400034044 sf0400033044 4 34044 4.81E-06 4.81E-06
vg0107057661 sf0107056661 1 7057661 4.88E-06 4.88E-06