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 mr1238 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
vg1125118463 sf1124652303 11 25118463 3.68E-31 2.57E-31
vg1124875808 sf1124409648 11 24875808 5.47E-12 6.00E-14
vg1124898092 sf1124431932 11 24898092 5.84E-11 2.34E-09
vg1124918104 sf1124451944 11 24918104 7.37E-11 8.68E-10
vg1124897169 sf1124431009 11 24897169 1.74E-08 7.06E-12
vg1124914537 sf1124448377 11 24914537 2.09E-08 7.76E-13
vg0814644208 sf0814641494 8 14644208 5.67E-08 2.43E-07
vg0307820737 sf0307819675 3 7820737 6.76E-07 2.30E-06
vg0224273930 sf0224268061 2 24273930 1.65E-06 4.75E-07
vg0106089280 sf0106088280 1 6089280 3.80E-06 2.85E-07
vg0721634662 sf0721633669 7 21634662 4.01E-06 4.01E-06
vg0328637867 sf0328630920 3 28637867 5.79E-06 2.19E-06
vg1124931687 sf1124465527 11 24931687 7.27E-06 5.27E-08
vg1124948132 sf1124481972 11 24948132 7.88E-06 2.38E-08
vg0901835907 sf0901834907 9 1835907 9.66E-06 1.04E-06
vg1125038779 sf1124572619 11 25038779 NA 1.10E-06
vg0208287795 sf0208287794 2 8287795 NA 1.17E-06
vg1124975706 sf1124509546 11 24975706 NA 1.18E-06
vg1125257848 sf1124791688 11 25257848 NA 2.87E-06