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 mr1519 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
vg0115224388 sf0115223362 1 15224388 4.39E-66 2.14E-13
vg0117911485 sf0117910439 1 17911485 2.76E-56 2.60E-08
vg0117972404 sf0117971358 1 17972404 3.63E-56 2.16E-08
vg0109389615 sf0109388591 1 9389615 6.54E-54 2.34E-08
vg0303387842 sf0303386838 3 3387842 9.59E-50 NA
vg0302782590 sf0302781586 3 2782590 1.59E-49 7.60E-07
vg0821686894 sf0821684181 8 21686894 1.71E-49 NA
vg0115147411 sf0115146385 1 15147411 NA 2.63E-17
vg0117665352 sf0117664306 1 17665352 NA 4.23E-12
vg1205988878 sf1205987859 12 5988878 NA 2.60E-08
vg0114752997 sf0114751971 1 14752997 NA 3.53E-08
vg0114394801 sf0114393775 1 14394801 NA 3.77E-08
vg0320043666 sf0320042177 3 20043666 NA 7.54E-08
vg0528836237 sf0528773592 5 28836237 NA 9.57E-08
vg0715489455 sf0715488462 7 15489455 NA 4.65E-07
vg1119865643 sf1119399566 11 19865643 NA 5.42E-07
vg0814797975 sf0814795261 8 14797975 NA 8.56E-07
vg0142245153 sf0142244109 1 42245153 NA 1.27E-06
vg0315264922 sf0315263569 3 15264922 NA 1.31E-06
vg0113946199 sf0113945173 1 13946199 NA 1.31E-06
vg0910741585 sf0910740584 9 10741585 NA 2.40E-06
vg0119921823 sf0119920778 1 19921823 NA 3.44E-06
vg0726435464 sf0726434470 7 26435464 NA 4.01E-06
vg0412900448 sf0412891156 4 12900448 NA 4.41E-06
vg1008185143 sf1008114005 10 8185143 NA 4.83E-06
vg0819248211 sf0819245498 8 19248211 NA 7.40E-06