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 mr1533 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
vg1013626874 sf1013555644 10 13626874 3.14E-98 2.09E-41
vg1013533412 sf1013462182 10 13533412 1.33E-84 5.10E-43
vg1013704036 sf1013632805 10 13704036 2.06E-54 1.46E-26
vg0315146805 sf0315145452 3 15146805 1.15E-45 NA
vg1016196833 sf1016125605 10 16196833 2.71E-45 NA
vg1006075286 sf1006091824 10 6075286 3.20E-45 NA
vg0107091002 sf0107090002 1 7091002 9.76E-45 NA
vg1013546417 sf1013475187 10 13546417 NA 6.87E-25
vg1013482483 sf1013411253 10 13482483 NA 9.63E-17
vg1013275569 sf1013204339 10 13275569 NA 5.23E-15
vg1013634835 sf1013563604 10 13634835 NA 1.18E-13
vg1013103415 sf1013032230 10 13103415 NA 2.75E-12
vg1013802723 sf1013731492 10 13802723 NA 5.50E-11
vg1013793084 sf1013721853 10 13793084 NA 1.04E-08
vg1013687229 sf1013615998 10 13687229 NA 3.46E-07
vg0817677081 sf0817674368 8 17677081 NA 1.60E-06
vg0142534585 sf0142533541 1 42534585 NA 1.79E-06
vg1126962405 sf1126490792 11 26962405 NA 2.50E-06
vg1013821799 sf1013750568 10 13821799 NA 2.73E-06