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 mr1561 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
vg0123668591 sf0123667547 1 23668591 3.99E-14 8.54E-06
vg0307000761 sf0306999759 3 7000761 6.46E-12 NA
vg1126542743 sf1126071158 11 26542743 1.13E-11 4.06E-10
vg1127031755 sf1126560142 11 27031755 3.67E-11 2.95E-07
vg0300484981 sf0300483979 3 484981 4.12E-11 NA
vg0601609792 sf0601608793 6 1609792 1.46E-09 NA
vg0402663053 sf0402658657 4 2663053 6.90E-09 4.67E-06
vg0516005213 sf0515947721 5 16005213 1.62E-08 NA
vg0819763162 sf0819760449 8 19763162 3.75E-08 NA
vg0122413949 sf0122412904 1 22413949 1.40E-07 8.48E-06
vg0625306076 sf0625305079 6 25306076 1.30E-06 NA