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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 mr1025 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
vg0907577141 sf0907576141 9 7577141 7.56E-07 7.56E-07
vg0107829215 sf0107828215 1 7829215 1.35E-06 1.35E-06
vg0702566842 sf0702565843 7 2566842 1.42E-06 1.42E-06
vg1119032991 sf1118566679 11 19032991 1.81E-06 1.81E-06
vg1207192862 sf1207190252 12 7192862 1.89E-06 1.89E-06
vg1218428323 sf1218399759 12 18428323 2.58E-06 2.58E-06
vg0210290709 sf0210290707 2 10290709 3.07E-06 3.07E-06
vg0222033395 sf0222027526 2 22033395 4.19E-06 4.19E-06
vg0906481295 sf0906480295 9 6481295 5.39E-06 5.39E-06