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 mr1104 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
vg0719039736 sf0719038743 7 19039736 3.42E-22 1.84E-19
vg0719040385 sf0719039392 7 19040385 9.45E-22 2.72E-19
vg0418036086 sf0417864127 4 18036086 6.29E-09 7.77E-06
vg0405725035 sf0405720474 4 5725035 1.93E-08 NA
vg0315197792 sf0315196439 3 15197792 2.17E-08 NA
vg0721979371 sf0721978378 7 21979371 2.51E-08 NA
vg0719125702 sf0719124709 7 19125702 2.53E-08 7.97E-13
vg0719141838 sf0719140845 7 19141838 9.92E-07 4.24E-11
vg0521133620 sf0521071061 5 21133620 1.15E-06 5.84E-07
vg1101991503 sf1101987361 11 1991503 NA 2.93E-07
vg0624049629 sf0624048632 6 24049629 NA 1.84E-06
vg0408294186 sf0408289460 4 8294186 NA 1.92E-06
vg0417642687 sf0417470728 4 17642687 NA 3.19E-06
vg0124676757 sf0124675713 1 24676757 NA 3.48E-06