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 mr1055 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
vg1215965939 sf1215963235 12 15965939 3.86E-136 4.93E-74
vg1210217896 sf1210215308 12 10217896 2.10E-56 NA
vg1212938220 sf1212935559 12 12938220 3.16E-47 1.46E-07
vg1224007541 sf1223973994 12 24007541 9.65E-46 NA
vg0216964004 sf0216958134 2 16964004 9.07E-45 NA
vg1215871396 sf1215868692 12 15871396 2.11E-35 4.25E-35
vg1212873997 sf1212871336 12 12873997 3.91E-35 3.93E-08
vg1215970855 sf1215968151 12 15970855 NA 5.45E-21
vg1215871822 sf1215869118 12 15871822 NA 7.36E-16
vg1216151755 sf1216149051 12 16151755 NA 1.47E-10
vg0610620315 sf0610619316 6 10620315 NA 3.21E-10
vg1216413575 sf1216410868 12 16413575 NA 8.62E-10
vg1216062863 sf1216060159 12 16062863 NA 1.12E-09
vg1216165057 sf1216162353 12 16165057 NA 1.74E-09
vg1216346096 sf1216343392 12 16346096 NA 2.56E-09
vg1109226985 sf1109221562 11 9226985 NA 4.98E-09
vg1215770747 sf1215768044 12 15770747 NA 1.81E-08
vg1216344388 sf1216341684 12 16344388 NA 2.65E-08
vg0521485463 sf0521422904 5 21485463 NA 3.36E-08
vg0401349008 sf0401344558 4 1349008 NA 4.78E-08
vg1215273070 sf1215270368 12 15273070 NA 5.77E-08
vg1117717695 sf1117251551 11 17717695 NA 6.76E-08
vg1212876949 sf1212874288 12 12876949 NA 9.76E-08
vg1215271479 sf1215268777 12 15271479 NA 1.24E-07