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 mr1852 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
vg1124078257 sf1123612127 11 24078257 1.21E-08 1.21E-08
vg1124078018 sf1123611888 11 24078018 3.87E-08 3.87E-08
vg0710771920 sf0710770926 7 10771920 4.61E-07 4.61E-07
vg0235593093 sf0235587224 2 35593093 9.17E-07 9.17E-07
vg0103381628 sf0103380628 1 3381628 1.35E-06 1.35E-06
vg1105377831 sf1105373582 11 5377831 1.42E-06 1.42E-06
vg1219984133 sf1219955575 12 19984133 2.01E-06 2.01E-06
vg0223168818 sf0223162949 2 23168818 2.07E-06 2.07E-06
vg0711805867 sf0711804873 7 11805867 3.19E-06 3.19E-06
vg0710985476 sf0710984482 7 10985476 4.17E-06 4.17E-06