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 mr1429 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
vg0224868229 sf0224862360 2 24868229 1.47E-08 1.48E-08
vg1107376701 sf1107372446 11 7376701 9.13E-08 9.17E-08
vg0420600418 sf0420428462 4 20600418 1.90E-07 1.91E-07
vg0622673582 sf0622672585 6 22673582 9.08E-07 9.12E-07
vg0224592034 sf0224586165 2 24592034 1.72E-06 1.71E-06
vg0715939840 sf0715938847 7 15939840 1.73E-06 1.73E-06
vg0804179427 sf0804178430 8 4179427 1.97E-06 1.98E-06
vg0501533978 sf0501533962 5 1533978 2.14E-06 2.15E-06
vg1222744855 sf1222711294 12 22744855 2.15E-06 2.15E-06
vg0327302530 sf0327295583 3 27302530 2.82E-06 2.84E-06
vg0717478015 sf0717477022 7 17478015 4.32E-06 4.34E-06
vg0430805986 sf0430620863 4 30805986 4.32E-06 4.34E-06
vg0222392097 sf0222386228 2 22392097 4.72E-06 4.74E-06