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 mr1697 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
vg0222337580 sf0222331711 2 22337580 8.13E-09 8.13E-09
vg0219780702 sf0219774834 2 19780702 4.97E-08 4.97E-08
vg0321576069 sf0321574579 3 21576069 1.09E-07 1.09E-07
vg0626069357 sf0626068360 6 26069357 2.12E-07 2.12E-07
vg0901536547 sf0901535547 9 1536547 1.80E-06 1.80E-06
vg0107079035 sf0107078035 1 7079035 1.87E-06 1.87E-06
vg0826077942 sf0826075228 8 26077942 2.54E-06 2.54E-06
vg1125042488 sf1124576328 11 25042488 3.29E-06 3.29E-06