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 mr1700 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
vg0400215019 sf0400214019 4 215019 8.04E-21 NA
vg0406944023 sf0406939291 4 6944023 1.80E-20 NA
vg0420778366 sf0420606409 4 20778366 2.82E-20 NA
vg0614984300 sf0614983301 6 14984300 7.05E-20 NA
vg0715986280 sf0715985287 7 15986280 9.94E-20 NA
vg0402100710 sf0402096304 4 2100710 5.08E-16 3.97E-06
vg1128511488 sf1127988267 11 28511488 NA 2.20E-07
vg0910768444 sf0910767443 9 10768444 NA 3.35E-06
vg1105433765 sf1105429516 11 5433765 NA 3.56E-06