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 mr1278 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
vg0717125075 sf0717124082 7 17125075 1.78E-09 4.86E-06
vg1020531763 sf1020460242 10 20531763 4.49E-09 7.09E-07
vg0608005446 sf0608004447 6 8005446 4.53E-09 2.38E-06
vg0726559146 sf0726558152 7 26559146 6.22E-09 2.63E-07
vg0220342715 sf0220336847 2 20342715 1.20E-08 3.41E-06
vg0801628860 sf0801627862 8 1628860 2.64E-08 4.79E-06
vg0717081055 sf0717080062 7 17081055 6.26E-08 5.68E-06
vg0516508609 sf0516451091 5 16508609 NA 1.04E-06
vg0607980327 sf0607979328 6 7980327 NA 1.48E-06
vg0817557507 sf0817554793 8 17557507 NA 1.77E-06
vg0420718113 sf0420546156 4 20718113 NA 2.51E-06
vg0516381476 sf0516323958 5 16381476 NA 3.68E-06
vg0235581681 sf0235575812 2 35581681 NA 4.96E-06
vg1215307750 sf1215305048 12 15307750 NA 4.99E-06