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 mr1934 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
vg0524788777 sf0524726192 5 24788777 1.59E-42 8.32E-24
vg0524615512 sf0524552932 5 24615512 1.75E-42 9.09E-24
vg1100144812 sf1100143813 11 144812 2.24E-17 NA
vg0604087909 sf0604086910 6 4087909 3.92E-16 NA
vg0230082779 sf0230076910 2 30082779 9.00E-14 NA
vg1200003632 sf1200002632 12 3632 1.28E-12 NA
vg1100016479 sf1100015479 11 16479 1.64E-12 3.31E-06
Unknow sf0427727822 Unknow Unknow 1.27E-11 NA
vg0601598971 sf0601597972 6 1598971 2.07E-10 3.99E-07
vg0822365872 sf0822363159 8 22365872 5.35E-10 3.02E-06
vg0605931332 sf0605930333 6 5931332 4.42E-09 2.52E-06