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 mr1673 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
vg1213717956 sf1213715294 12 13717956 2.52E-08 2.52E-08
vg1213717963 sf1213715301 12 13717963 7.61E-08 7.61E-08
vg0416689969 sf0416518012 4 16689969 6.44E-07 6.44E-07
vg1214787900 sf1214785241 12 14787900 1.23E-06 1.23E-06
vg0908229421 sf0908228421 9 8229421 1.54E-06 1.54E-06
vg1102677343 sf1102673247 11 2677343 2.97E-06 2.97E-06
vg0901583779 sf0901582779 9 1583779 4.24E-06 4.24E-06
vg0223263891 sf0223258022 2 23263891 4.91E-06 4.91E-06