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 mr1517 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
vg0137855094 sf0137854051 1 37855094 2.20E-18 2.15E-14
vg1121707705 sf1121241582 11 21707705 1.10E-10 4.87E-07
vg0806945854 sf0806944859 8 6945854 1.55E-09 NA
vg1126565937 sf1126094352 11 26565937 2.10E-09 8.86E-06
vg1128914308 sf1128391087 11 28914308 4.17E-09 NA
vg0727484366 sf0727483372 7 27484366 8.51E-09 1.23E-07
vg1122062891 sf1121596762 11 22062891 2.02E-07 2.62E-06
vg0235270915 sf0235265046 2 35270915 4.33E-07 1.71E-06
vg1118403739 sf1117937599 11 18403739 6.28E-07 1.48E-06
vg0134690705 sf0134689662 1 34690705 1.00E-06 6.65E-08
vg0608120267 sf0608119268 6 8120267 NA 2.84E-07
vg0228130479 sf0228124610 2 28130479 NA 2.86E-07