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 mr1550 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
vg0705425288 sf0705424289 7 5425288 2.04E-10 4.88E-10
vg0400004808 sf0400003808 4 4808 2.76E-10 4.15E-07
vg0705438086 sf0705437087 7 5438086 5.34E-10 8.11E-11
vg0500370570 sf0500370570 5 370570 2.59E-08 NA
vg0602872794 sf0602871795 6 2872794 3.02E-08 1.04E-06
vg0234416765 sf0234410896 2 34416765 3.41E-08 4.93E-06
vg0209288014 sf0209288012 2 9288014 1.05E-07 4.26E-06
vg0906350119 sf0906349119 9 6350119 2.42E-07 1.98E-06
vg0729061858 sf0729060866 7 29061858 3.34E-07 3.80E-06
vg0406007518 sf0406002957 4 6007518 6.89E-07 2.98E-06
vg0411851800 sf0411842511 4 11851800 1.06E-06 2.02E-06
vg0812497333 sf0812496237 8 12497333 NA 8.48E-07
vg1127364602 sf1126892989 11 27364602 NA 8.71E-07