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 mr1072 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
vg0222727819 sf0222721950 2 22727819 1.82E-40 2.05E-23
vg0223683609 sf0223677740 2 23683609 5.71E-15 5.70E-08
vg0223537448 sf0223531579 2 23537448 4.56E-13 1.17E-07
vg0223453927 sf0223448058 2 23453927 1.48E-11 NA
vg0225446728 sf0225440859 2 25446728 3.37E-11 1.55E-06
vg1112606104 sf1112142307 11 12606104 3.38E-11 NA
vg0222624829 sf0222618960 2 22624829 6.66E-11 5.32E-08
vg0226049138 sf0226043269 2 26049138 4.78E-10 3.42E-06
vg0224275719 sf0224269850 2 24275719 3.82E-09 1.91E-06
vg0222857256 sf0222851387 2 22857256 1.16E-08 2.29E-06
vg0222671915 sf0222666046 2 22671915 2.43E-08 3.58E-09
vg0601227919 sf0601226920 6 1227919 3.03E-07 NA
vg0224432425 sf0224426556 2 24432425 NA 9.26E-06