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 mr1679 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
vg1002807953 sf1002806930 10 2807953 1.71E-12 NA
vg0720805926 sf0720804933 7 20805926 1.64E-11 1.05E-11
vg0719727009 sf0719726016 7 19727009 3.12E-11 NA
vg0315905274 sf0315903921 3 15905274 4.80E-11 NA
vg0519574036 sf0519511520 5 19574036 5.33E-11 NA
vg1204725380 sf1204724365 12 4725380 5.65E-11 4.57E-08
vg1223901098 sf1223867551 12 23901098 1.14E-09 7.05E-08
vg0507287869 sf0507287811 5 7287869 5.37E-09 4.41E-06
vg0316718408 sf0316717054 3 16718408 8.44E-09 7.42E-07
vg1119581692 sf1119115380 11 19581692 NA 2.03E-07
vg0427914020 sf0427728883 4 27914020 NA 1.04E-06
vg0225231134 sf0225225265 2 25231134 NA 1.45E-06
vg1204824887 sf1204823872 12 4824887 NA 1.77E-06
vg0609471975 sf0609470976 6 9471975 NA 6.74E-06