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 mr1277 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
vg0800302779 sf0800301779 8 302779 1.64E-16 3.74E-12
vg0800219246 sf0800218246 8 219246 1.97E-15 1.96E-12
vg0800160344 sf0800159344 8 160344 3.87E-11 3.13E-13
vg1112894682 sf1112431003 11 12894682 5.02E-10 5.21E-06
vg1112762176 sf1112298497 11 12762176 1.05E-09 1.61E-06
vg1112778612 sf1112314933 11 12778612 4.03E-09 NA
vg0700004041 sf0700003041 7 4041 9.65E-09 1.48E-06
vg1109175716 sf1109170295 11 9175716 2.21E-08 NA
vg0308604272 sf0308603210 3 8604272 2.14E-06 NA
vg0206101249 sf0206101249 2 6101249 7.89E-06 4.94E-06
vg0800272949 sf0800271949 8 272949 NA 3.05E-06
vg0323714977 sf0323713151 3 23714977 NA 5.97E-06
vg1011535971 sf1011464790 10 11535971 NA 9.48E-06