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 mr1241 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
vg0604233838 sf0604232839 6 4233838 2.72E-83 4.13E-17
vg0719064331 sf0719063338 7 19064331 1.60E-80 5.27E-16
vg0311189318 sf0311188036 3 11189318 9.94E-74 5.13E-08
vg0719199004 sf0719198011 7 19199004 3.83E-71 4.60E-15
vg0305852353 sf0305851353 3 5852353 2.78E-69 NA
vg1225138688 sf1225105142 12 25138688 1.17E-68 NA
vg0626833038 sf0626832041 6 26833038 6.87E-66 3.59E-08
vg0139762608 sf0139761565 1 39762608 1.00E-65 3.30E-06
vg0326934528 sf0326927581 3 26934528 4.29E-63 2.78E-06
vg0134494360 sf0134493317 1 34494360 2.01E-62 1.04E-07
vg0430364870 sf0430179747 4 30364870 1.40E-60 1.63E-06
vg0304719097 sf0304718099 3 4719097 2.59E-59 6.33E-06
vg0917639240 sf0917638239 9 17639240 3.10E-59 3.90E-06
vg0719062695 sf0719061702 7 19062695 NA 7.32E-14
vg0719091461 sf0719090468 7 19091461 NA 1.38E-08
vg0604287754 sf0604286755 6 4287754 NA 7.23E-08
vg0228554225 sf0228548356 2 28554225 NA 7.85E-08
vg0804049852 sf0804048855 8 4049852 NA 8.99E-08
vg0722130735 sf0722129742 7 22130735 NA 1.58E-07
vg0306636968 sf0306635968 3 6636968 NA 3.31E-07
vg0135124935 sf0135123892 1 35124935 NA 3.65E-07
vg0604242610 sf0604241611 6 4242610 NA 4.18E-07
vg1111092734 sf1111087051 11 11092734 NA 5.64E-07
vg0716398948 sf0716397955 7 16398948 NA 6.61E-07
vg1222822194 sf1222788633 12 22822194 NA 8.61E-07
vg1215239496 sf1215236793 12 15239496 NA 9.38E-07
vg0828401472 sf0828398758 8 28401472 NA 1.07E-06
vg0315302686 sf0315301333 3 15302686 NA 1.18E-06
vg0431879764 sf0431694659 4 31879764 NA 3.36E-06
vg0228497476 sf0228491607 2 28497476 NA 3.70E-06