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 mr1405 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
vg0810864582 sf0810863587 8 10864582 2.12E-08 1.67E-06
vg0128433127 sf0128432082 1 28433127 6.13E-08 NA
vg0810647541 sf0810646545 8 10647541 6.20E-08 9.92E-07
vg0816276539 sf0816273825 8 16276539 4.50E-07 7.40E-07
vg0725508857 sf0725507863 7 25508857 9.20E-07 6.61E-06
vg0419763927 sf0419591962 4 19763927 1.17E-06 1.22E-06