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 mr1648 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
vg0506138324 sf0506138263 5 6138324 4.28E-11 NA
vg0601158634 sf0601157635 6 1158634 4.86E-10 NA
vg0822545105 sf0822542392 8 22545105 5.79E-10 8.94E-07
vg0710562047 sf0710561053 7 10562047 7.51E-10 1.34E-06
vg0112234029 sf0112233003 1 12234029 1.08E-09 NA
vg0906793623 sf0906792623 9 6793623 1.24E-09 7.61E-06
vg0519953159 sf0519890635 5 19953159 5.68E-09 4.94E-06
vg0630762253 sf0630761255 6 30762253 3.63E-08 1.17E-06
vg0511944956 sf0511944886 5 11944956 4.78E-08 1.25E-06
vg0203767835 sf0203767832 2 3767835 1.73E-07 1.59E-06
vg0421213186 sf0421041238 4 21213186 5.39E-07 8.15E-07
vg0214233942 sf0214228072 2 14233942 2.26E-06 NA
vg0119464019 sf0119462974 1 19464019 5.32E-06 1.61E-06
vg1224673904 sf1224640358 12 24673904 NA 2.75E-06