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 mr1436 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
vg0719011406 sf0719010413 7 19011406 2.01E-12 1.00E-10
vg0431298868 sf0431113758 4 31298868 1.19E-10 1.85E-07
vg0717227488 sf0717226495 7 17227488 2.00E-10 2.09E-07
vg0717217051 sf0717216058 7 17217051 2.28E-10 8.20E-08
vg0717368185 sf0717367192 7 17368185 1.72E-09 NA
vg0719003833 sf0719002840 7 19003833 2.20E-09 6.51E-07
vg1201582442 sf1201581442 12 1582442 5.00E-09 1.48E-06
vg0401795249 sf0401790844 4 1795249 4.67E-08 4.95E-06
vg0226057933 sf0226052064 2 26057933 1.38E-07 1.08E-06
vg0600352193 sf0600351193 6 352193 1.23E-06 NA
vg1121617620 sf1121151497 11 21617620 2.12E-06 4.67E-06
vg1207833484 sf1207830890 12 7833484 4.76E-06 1.81E-06
vg1208420591 sf1208417997 12 8420591 5.31E-06 NA
vg1007474523 sf1007490146 10 7474523 8.18E-06 1.21E-06
vg1009450763 sf1009379584 10 9450763 NA 4.12E-06
vg0824785295 sf0824782581 8 24785295 NA 9.40E-06