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 mr1558 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
vg1020424844 sf1020353323 10 20424844 4.04E-93 1.12E-19
vg1020420315 sf1020348794 10 20420315 1.13E-86 7.21E-22
vg0132864766 sf0132863722 1 32864766 2.38E-69 3.34E-06
vg0130114438 sf0130113393 1 30114438 3.38E-69 7.86E-06
vg0305747943 sf0305746943 3 5747943 9.43E-68 NA
vg0705569582 sf0705568583 7 5569582 4.58E-67 NA
vg0434389908 sf0434204802 4 34389908 3.77E-62 3.63E-07
vg0434782748 sf0434597639 4 34782748 NA 4.56E-07
vg1209415105 sf1209412514 12 9415105 NA 8.31E-07
vg1122436158 sf1121970029 11 22436158 NA 1.56E-06
vg1209327674 sf1209325083 12 9327674 NA 1.60E-06
vg0323951924 sf0323950098 3 23951924 NA 3.11E-06
vg1209694733 sf1209692142 12 9694733 NA 4.22E-06