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 mr1017 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
vg1215976937 sf1215974233 12 15976937 1.48E-128 5.68E-63
vg1215965939 sf1215963235 12 15965939 2.36E-128 3.84E-63
vg1210217896 sf1210215308 12 10217896 3.02E-57 NA
vg1224007541 sf1223973994 12 24007541 2.52E-48 NA
vg0216964004 sf0216958134 2 16964004 3.95E-45 NA
vg1213439981 sf1213437319 12 13439981 9.73E-45 6.28E-06
vg1219373193 sf1219344662 12 19373193 6.95E-41 2.85E-08
vg1212873997 sf1212871336 12 12873997 4.14E-34 1.12E-07
vg1215871396 sf1215868692 12 15871396 NA 1.02E-28
vg1215970855 sf1215968151 12 15970855 NA 3.72E-18
vg1215871822 sf1215869118 12 15871822 NA 4.06E-16
vg0521485463 sf0521422904 5 21485463 NA 3.48E-09
vg1216151755 sf1216149051 12 16151755 NA 4.68E-09
vg1216062863 sf1216060159 12 16062863 NA 6.55E-09
vg1216165057 sf1216162353 12 16165057 NA 2.12E-08
vg0432166518 sf0431981411 4 32166518 NA 5.61E-08
vg0610620315 sf0610619316 6 10620315 NA 8.27E-08
vg1215283366 sf1215280664 12 15283366 NA 8.63E-08
vg1215962650 sf1215959946 12 15962650 NA 3.09E-07
vg1216413575 sf1216410868 12 16413575 NA 4.34E-07
vg1216346285 sf1216343581 12 16346285 NA 7.22E-07
vg1215978234 sf1215975530 12 15978234 NA 7.71E-07
vg1217371642 sf1217365597 12 17371642 NA 7.85E-07
vg1209593460 sf1209590869 12 9593460 NA 9.18E-07
vg1215808919 sf1215806216 12 15808919 NA 1.06E-06
vg1216416569 sf1216413862 12 16416569 NA 1.23E-06