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 mr1079 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
vg1215977007 sf1215974303 12 15977007 6.05E-168 2.61E-57
vg1216261222 sf1216258518 12 16261222 6.96E-103 1.63E-30
vg1210337904 sf1210335317 12 10337904 3.90E-81 NA
vg1212938220 sf1212935559 12 12938220 1.28E-71 NA
vg1224007541 sf1223973994 12 24007541 6.27E-70 NA
vg0217066401 sf0217060531 2 17066401 6.32E-62 NA
vg1223898851 sf1223865304 12 23898851 7.81E-57 1.96E-09
vg1215871396 sf1215868692 12 15871396 NA 4.54E-30
vg1215871822 sf1215869118 12 15871822 NA 1.36E-12
vg1215969757 sf1215967053 12 15969757 NA 2.62E-12
vg0610620315 sf0610619316 6 10620315 NA 3.36E-11
vg1217327067 sf1217321022 12 17327067 NA 6.25E-11
vg1215763538 sf1215760835 12 15763538 NA 1.15E-10
vg1216486981 sf1216484274 12 16486981 NA 3.18E-10
vg1216037905 sf1216035201 12 16037905 NA 1.25E-09
vg1216151755 sf1216149051 12 16151755 NA 2.87E-09
vg1215976560 sf1215973856 12 15976560 NA 1.06E-08
vg1215321806 sf1215319104 12 15321806 NA 1.95E-08
vg1215886454 sf1215883750 12 15886454 NA 2.35E-08
vg1216413575 sf1216410868 12 16413575 NA 3.51E-08
vg1215962650 sf1215959946 12 15962650 NA 5.83E-08
vg0123696065 sf0123695021 1 23696065 NA 7.17E-08
vg1215800900 sf1215798197 12 15800900 NA 1.11E-07
vg0123689616 sf0123688572 1 23689616 NA 2.04E-07
vg1214868017 sf1214865358 12 14868017 NA 2.09E-07
vg0408410810 sf0408406084 4 8410810 NA 2.90E-07
vg1216550268 sf1216547561 12 16550268 NA 3.66E-06