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
vg0604215476 sf0604214477 6 4215476 3.31E-20 3.66E-08
vg0604254993 sf0604253994 6 4254993 2.45E-19 1.14E-07
vg0311223124 sf0311221842 3 11223124 8.33E-18 5.69E-06
vg0432212638 sf0432027530 4 32212638 2.39E-17 8.81E-06
vg0311203948 sf0311202666 3 11203948 3.51E-17 3.96E-06
vg0132286257 sf0132285213 1 32286257 6.11E-17 NA
vg0204716570 sf0204716567 2 4716570 6.84E-17 NA
vg0719062695 sf0719061702 7 19062695 4.12E-16 2.75E-10
vg0432065258 sf0431880150 4 32065258 1.81E-14 4.48E-06
vg0134494360 sf0134493317 1 34494360 1.85E-14 1.94E-07
vg0820065663 sf0820062950 8 20065663 NA 7.79E-07
vg0719053396 sf0719052403 7 19053396 NA 1.16E-06
vg0626895745 sf0626894748 6 26895745 NA 1.83E-06
vg1016056141 sf1015984913 10 16056141 NA 1.99E-06
vg0432569098 sf0432383989 4 32569098 NA 2.92E-06