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 mr1410 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
vg1214659401 sf1214656741 12 14659401 7.63E-23 1.62E-10
vg1214631678 sf1214629018 12 14631678 7.79E-23 1.48E-10
vg1210452682 sf1210450095 12 10452682 1.03E-20 6.53E-09
vg1217441137 sf1217435092 12 17441137 1.80E-19 1.09E-08
vg0215909137 sf0215903267 2 15909137 3.48E-18 3.03E-06
vg0805104616 sf0805103619 8 5104616 1.09E-17 NA
vg0820664167 sf0820661454 8 20664167 1.44E-17 7.11E-07
vg1017600508 sf1017529281 10 17600508 3.17E-17 2.83E-06
vg0919562382 sf0919561972 9 19562382 1.97E-14 3.29E-07
vg0806319094 sf0806318099 8 6319094 2.94E-14 3.28E-06
vg1200249590 sf1200248590 12 249590 NA 3.72E-07
vg0617821096 sf0617820099 6 17821096 NA 4.00E-07
vg0504497766 sf0504497743 5 4497766 NA 1.77E-06
vg0706567685 sf0706566690 7 6567685 NA 2.51E-06
vg0619386162 sf0619385165 6 19386162 NA 4.57E-06
vg0617915677 sf0617914680 6 17915677 NA 4.74E-06
vg0527519592 sf0527456948 5 27519592 NA 6.68E-06