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 mr1494 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
vg0220479392 sf0220473524 2 20479392 2.20E-07 2.20E-07
vg0220430651 sf0220424783 2 20430651 2.95E-07 2.95E-07
vg0918774898 sf0918773898 9 18774898 5.68E-07 5.68E-07
vg0232486002 sf0232480133 2 32486002 1.47E-06 1.47E-06
vg0805108529 sf0805107532 8 5108529 2.54E-06 2.54E-06
vg0102103204 sf0102102204 1 2103204 2.86E-06 2.86E-06
vg0232482432 sf0232476563 2 32482432 3.49E-06 3.49E-06
vg0220319668 sf0220313800 2 20319668 3.93E-06 3.93E-06
vg0227468030 sf0227462161 2 27468030 4.36E-06 4.36E-06