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 mr1565 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
vg0142065897 sf0142064854 1 42065897 1.12E-15 NA
vg0400907136 sf0400906136 4 907136 1.98E-15 NA
vg1101821019 sf1101820020 11 1821019 2.80E-15 NA
vg1203000072 sf1202999074 12 3000072 7.77E-15 NA
vg0302528593 sf0302527589 3 2528593 8.60E-15 NA
vg0400373812 sf0400372810 4 373812 4.33E-13 2.66E-06
vg1217642122 sf1217636077 12 17642122 6.35E-10 6.90E-07
vg0401153085 sf0401148635 4 1153085 NA 2.45E-07
vg0226676076 sf0226670207 2 26676076 NA 1.71E-06
vg1207772422 sf1207769828 12 7772422 NA 2.64E-06