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 mr1896 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
vg0524718407 sf0524655827 5 24718407 1.73E-30 1.80E-17
vg0524598675 sf0524536095 5 24598675 9.12E-30 2.21E-18
vg1100144812 sf1100143813 11 144812 9.41E-16 9.36E-06
vg0524331456 sf0524268875 5 24331456 1.00E-13 4.34E-06
vg1100016479 sf1100015479 11 16479 1.58E-11 7.91E-07
vg0433393939 sf0433208828 4 33393939 2.54E-11 NA
vg0218379007 sf0218373138 2 18379007 5.15E-11 NA
vg0229918162 sf0229912293 2 29918162 2.61E-09 1.65E-06
vg0726455758 sf0726454764 7 26455758 1.68E-06 NA
vg0430128516 sf0429943387 4 30128516 3.48E-06 NA
vg0217028559 sf0217022689 2 17028559 4.24E-06 2.55E-06
vg0216675557 sf0216669687 2 16675557 NA 2.52E-06