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 mr1899 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
vg0107647091 sf0107646091 1 7647091 1.77E-09 3.22E-11
vg0210785841 sf0210785839 2 10785841 1.60E-08 NA
vg0300247343 sf0300246343 3 247343 2.10E-08 NA
vg0803208493 sf0803207496 8 3208493 5.19E-08 NA
vg0916047184 sf0916046183 9 16047184 6.55E-08 NA
vg1002940641 sf1002939618 10 2940641 1.54E-07 NA
vg0801912932 sf0801911935 8 1912932 4.37E-07 NA
vg0316262550 sf0316261197 3 16262550 6.57E-07 4.05E-06
vg0617087390 sf0617086393 6 17087390 8.86E-07 NA
vg0501568601 sf0501568585 5 1568601 1.07E-06 1.34E-06
vg1217053914 sf1217047868 12 17053914 2.49E-06 3.15E-07
vg0218008797 sf0218002928 2 18008797 9.45E-06 NA
vg1002941120 sf1002940097 10 2941120 NA 2.86E-06