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 mr1156 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
vg1216400232 sf1216397525 12 16400232 8.12E-12 NA
vg1000061236 sf1000060236 10 61236 3.61E-11 NA
vg1210564472 sf1210561885 12 10564472 3.86E-11 NA
vg1016837158 sf1016765930 10 16837158 1.80E-10 NA
vg0915690278 sf0915689277 9 15690278 2.74E-10 NA
vg1213283850 sf1213281188 12 13283850 4.94E-09 1.38E-06
vg1126966038 sf1126494425 11 26966038 2.74E-06 NA
vg1216321299 sf1216318595 12 16321299 NA 2.05E-06