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 mr1669 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
vg0704732672 sf0704731673 7 4732672 2.30E-10 1.03E-08
vg0709448532 sf0709447538 7 9448532 2.64E-10 3.17E-08
vg0713442761 sf0713441768 7 13442761 6.37E-09 1.74E-07
vg0717122365 sf0717121372 7 17122365 8.55E-09 NA
vg0141969878 sf0141968835 1 41969878 4.23E-08 3.02E-07
vg0421384856 sf0421212909 4 21384856 1.00E-07 4.16E-06
vg0322405319 sf0322403808 3 22405319 2.96E-07 2.45E-06
vg0516508609 sf0516451091 5 16508609 4.66E-07 2.34E-07
vg0328522871 sf0328515924 3 28522871 6.86E-07 4.27E-06
vg0516563624 sf0516506106 5 16563624 1.49E-06 3.07E-07
vg0403204105 sf0403199708 4 3204105 3.02E-06 4.97E-06
vg0322439061 sf0322437550 3 22439061 4.62E-06 1.29E-06
vg0421396071 sf0421224124 4 21396071 9.92E-06 NA