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
vg0800063298 sf0800062298 8 63298 2.16E-20 2.63E-12
vg0800035751 sf0800034751 8 35751 7.20E-18 6.08E-13
vg0800202591 sf0800201591 8 202591 3.18E-17 2.17E-11
vg0800300760 sf0800299760 8 300760 1.24E-15 5.82E-08
vg1113882833 sf1113419154 11 13882833 5.44E-15 NA
vg0801340528 sf0801339530 8 1340528 1.37E-13 1.07E-06
vg0601000809 sf0600999810 6 1000809 2.30E-13 NA
vg0801311224 sf0801310226 8 1311224 4.21E-13 5.24E-07
vg1017707464 sf1017636237 10 17707464 7.76E-12 NA
vg0800102374 sf0800101374 8 102374 1.96E-11 1.27E-07
vg0311534838 sf0311533556 3 11534838 6.74E-11 NA
vg0800225034 sf0800224034 8 225034 NA 1.00E-10
vg0801223463 sf0801222465 8 1223463 NA 1.06E-06
vg1113156043 sf1112692364 11 13156043 NA 4.08E-06