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 mr1819 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
vg0605513869 sf0605512870 6 5513869 9.33E-15 2.39E-09
vg0706559114 sf0706558119 7 6559114 3.67E-11 NA
vg0907175535 sf0907174535 9 7175535 7.46E-11 4.07E-07
vg1202865605 sf1202864607 12 2865605 7.55E-11 NA
vg1013810944 sf1013739713 10 13810944 8.05E-11 NA
vg0232755756 sf0232749887 2 32755756 3.19E-10 6.72E-08
vg0217637634 sf0217631764 2 17637634 7.29E-10 9.14E-07
vg0205955682 sf0205955682 2 5955682 5.94E-09 NA
vg0717056152 sf0717055159 7 17056152 1.01E-08 2.95E-06
vg0421497707 sf0421325758 4 21497707 5.10E-08 9.11E-07
vg1214600105 sf1214597445 12 14600105 NA 2.73E-06