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 mr1878 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
vg0719007567 sf0719006574 7 19007567 2.06E-12 1.43E-10
vg0626675544 sf0626674547 6 26675544 2.99E-10 3.47E-06
vg1201654412 sf1201653412 12 1654412 3.11E-09 3.36E-06
vg0707794523 sf0707793528 7 7794523 4.02E-09 NA
vg1201736330 sf1201735328 12 1736330 4.44E-09 2.99E-06
vg0626644874 sf0626643877 6 26644874 2.85E-08 NA
vg0224541228 sf0224535359 2 24541228 6.06E-07 NA
vg0718862824 sf0718861831 7 18862824 8.17E-07 1.67E-06
vg0719153233 sf0719152240 7 19153233 3.58E-06 3.07E-06
vg0718985954 sf0718984961 7 18985954 NA 3.69E-06