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 mr1756 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
vg0726964336 sf0726963342 7 26964336 8.67E-12 NA
vg0819604933 sf0819602220 8 19604933 3.07E-09 9.69E-06
vg0819603267 sf0819600554 8 19603267 4.22E-09 NA
vg1105571587 sf1105567339 11 5571587 6.11E-09 NA
vg1102432290 sf1102428194 11 2432290 6.75E-09 NA
vg1102442316 sf1102438220 11 2442316 9.12E-09 3.12E-06
vg0904129442 sf0904128442 9 4129442 1.18E-07 1.06E-06
vg0707346462 sf0707345467 7 7346462 5.71E-07 2.49E-06
vg1218867722 sf1218839157 12 18867722 8.70E-07 NA
vg0223634166 sf0223628297 2 23634166 3.08E-06 NA
vg0434331604 sf0434146498 4 34331604 4.09E-06 4.45E-06