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 mr1330 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
vg0822847284 sf0822844571 8 22847284 4.34E-11 2.81E-06
vg0207238898 sf0207238898 2 7238898 9.79E-11 NA
vg0315008841 sf0315007488 3 15008841 1.76E-10 NA
vg0725833077 sf0725832083 7 25833077 7.01E-10 NA
vg0431352110 sf0431167005 4 31352110 7.41E-10 NA
vg0619101816 sf0619100819 6 19101816 9.74E-10 2.45E-06
vg0618471057 sf0618470060 6 18471057 9.14E-09 NA
vg1000856390 sf1000855366 10 856390 5.29E-07 NA