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 mr1900 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 1.37E-24 3.63E-25
vg1124875808 sf1124409648 11 24875808 2.51E-13 4.17E-15
vg1124966900 sf1124500740 11 24966900 5.79E-09 3.39E-13
vg1124931687 sf1124465527 11 24931687 1.84E-08 2.44E-10
vg1124898092 sf1124431932 11 24898092 2.64E-08 4.54E-07
vg1124959837 sf1124493677 11 24959837 1.02E-07 4.40E-07
vg1125022392 sf1124556232 11 25022392 1.97E-07 1.51E-06
vg1214549363 sf1214546704 12 14549363 9.34E-07 3.35E-06
vg0717185752 sf0717184759 7 17185752 1.02E-06 4.72E-06
vg0328637867 sf0328630920 3 28637867 3.03E-06 3.18E-07
vg0721634662 sf0721633669 7 21634662 4.11E-06 3.58E-06
vg0208287795 sf0208287794 2 8287795 NA 4.71E-07
vg1124948132 sf1124481972 11 24948132 NA 8.98E-07
vg0106089280 sf0106088280 1 6089280 NA 1.51E-06
vg1124975706 sf1124509546 11 24975706 NA 2.14E-06