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 mr1968 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
vg0327933461 sf0327926515 3 27933461 1.16E-08 NA
vg1114854277 sf1114390591 11 14854277 8.03E-08 NA
vg0718117891 sf0718116898 7 18117891 8.84E-08 NA
vg1117567707 sf1117101564 11 17567707 9.34E-08 NA
vg0330602833 sf0330595722 3 30602833 9.73E-08 NA
vg0327937122 sf0327930176 3 27937122 4.50E-07 NA
vg0616660850 sf0616659852 6 16660850 8.46E-07 2.12E-06
vg0622686369 sf0622685372 6 22686369 5.00E-06 5.03E-07
vg0518299665 sf0518239151 5 18299665 6.09E-06 NA
vg0922490768 sf0922490287 9 22490768 8.28E-06 NA