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 mr1962 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 8.80E-44 5.85E-25
vg0222744532 sf0222738663 2 22744532 1.64E-43 4.59E-26
vg0224620773 sf0224614904 2 24620773 7.87E-17 1.15E-08
vg0223730720 sf0223724851 2 23730720 3.23E-15 1.48E-09
vg0223943227 sf0223937358 2 23943227 1.16E-14 NA
vg0229592697 sf0229586828 2 29592697 1.56E-13 NA
vg0120470627 sf0120469582 1 20470627 1.21E-12 NA
vg0222852276 sf0222846407 2 22852276 3.16E-12 1.28E-09
vg0225864108 sf0225858239 2 25864108 5.85E-10 2.01E-06
vg0225032737 sf0225026868 2 25032737 6.42E-10 3.95E-06
vg0222797604 sf0222791735 2 22797604 2.33E-09 2.57E-06
vg0222729132 sf0222723263 2 22729132 2.24E-08 4.86E-06
vg0121870570 sf0121869525 1 21870570 2.60E-07 NA
vg0223051176 sf0223045307 2 23051176 3.66E-07 2.66E-06
vg0131938048 sf0131937004 1 31938048 1.16E-06 NA
vg0222553841 sf0222547972 2 22553841 NA 2.02E-06
vg0224323458 sf0224317589 2 24323458 NA 2.56E-06
vg0407665649 sf0407660916 4 7665649 NA 4.95E-06