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 mr1803 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
vg0207779124 sf0207779123 2 7779124 4.02E-11 NA
vg1214831718 sf1214829059 12 14831718 5.92E-11 2.59E-07
vg0800557142 sf0800556142 8 557142 3.45E-10 NA
vg1220919709 sf1220886258 12 20919709 6.56E-10 1.43E-07
vg0805577321 sf0805576324 8 5577321 9.97E-10 NA
vg1214835725 sf1214833066 12 14835725 2.34E-09 9.63E-08
vg0811898736 sf0811897741 8 11898736 2.02E-08 NA
vg1209190546 sf1209187955 12 9190546 3.74E-08 2.97E-08
vg0609487743 sf0617686677 6 9487743 NA 2.61E-06