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 mr1850 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
vg0610463066 sf0610462067 6 10463066 3.63E-12 9.68E-07
vg0610026652 sf0610025653 6 10026652 6.33E-12 2.65E-07
vg1213210547 sf1213207885 12 13210547 2.84E-11 1.44E-06
vg0714048670 sf0714047677 7 14048670 3.83E-10 3.58E-06
vg0602091036 sf0602090037 6 2091036 9.52E-10 NA
vg0127823351 sf0127822307 1 27823351 1.17E-09 NA
vg0529112100 sf0529049455 5 29112100 1.95E-09 2.58E-06
vg0329650051 sf0329643091 3 29650051 2.44E-09 6.74E-07
vg0220268633 sf0220262765 2 20268633 6.67E-09 NA
vg0610861016 sf0610860017 6 10861016 6.94E-08 5.53E-06
vg0616146874 sf0616145876 6 16146874 6.77E-07 3.94E-06
vg0142799943 sf0142798899 1 42799943 NA 1.46E-07