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 mr1178 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
vg1215999852 sf1215997148 12 15999852 1.78E-26 2.34E-13
vg1011511779 sf1011440598 10 11511779 3.47E-16 9.08E-07
vg1011511526 sf1011440345 10 11511526 5.68E-16 1.13E-06
vg1006590352 sf1006605975 10 6590352 7.98E-14 NA
vg0722264977 sf0722263984 7 22264977 1.44E-13 NA
vg1213297058 sf1213294396 12 13297058 2.25E-13 NA
vg1018726980 sf1018655537 10 18726980 3.98E-12 4.67E-06
vg1006587700 sf1006603323 10 6587700 1.60E-10 3.77E-06
vg1216828835 sf1216822789 12 16828835 NA 2.62E-07
vg1206197673 sf1206196564 12 6197673 NA 5.66E-07
vg1209876216 sf1209873626 12 9876216 NA 4.36E-06