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 mr1632 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
vg0506946105 sf0506946047 5 6946105 2.40E-47 3.92E-14
vg0506847027 sf0506846969 5 6847027 3.45E-47 1.45E-14
vg0506871793 sf0506871735 5 6871793 1.45E-43 2.91E-27
vg0514684611 sf0514627154 5 14684611 1.25E-36 2.22E-06
vg0226661509 sf0226655640 2 26661509 3.25E-32 NA
vg0215278505 sf0215272635 2 15278505 4.85E-32 4.50E-07
vg0511003990 sf0511003919 5 11003990 NA 2.22E-13
vg1009362967 sf1009291788 10 9362967 NA 4.43E-12
vg0514650559 sf0514593102 5 14650559 NA 2.19E-11
vg1001247140 sf1001246117 10 1247140 NA 5.67E-11
vg0506708732 sf0506708674 5 6708732 NA 1.90E-07
vg0509049542 sf0509049470 5 9049542 NA 4.76E-07
vg0506924589 sf0506924531 5 6924589 NA 9.63E-07
vg0506490603 sf0506490544 5 6490603 NA 1.07E-06
vg1219819590 sf1219791060 12 19819590 NA 1.13E-06
vg0817398694 sf0817395980 8 17398694 NA 2.24E-06
vg0506904965 sf0506904907 5 6904965 NA 2.74E-06
vg1209223420 sf1209220829 12 9223420 NA 3.21E-06
vg0335019883 sf0335012753 3 35019883 NA 4.87E-06
vg1224152951 sf1224119405 12 24152951 NA 4.95E-06