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 mr1753 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
vg0714622950 sf0714621957 7 14622950 2.20E-08 2.20E-08
vg0819676808 sf0819674095 8 19676808 4.72E-08 4.73E-08
vg0819680240 sf0819677527 8 19680240 2.27E-07 2.27E-07
vg0709448532 sf0709447538 7 9448532 4.73E-07 4.73E-07
vg0122971925 sf0122970881 1 22971925 2.34E-06 2.34E-06
vg0704732672 sf0704731673 7 4732672 3.17E-06 3.17E-06
vg0714470576 sf0714469583 7 14470576 4.69E-06 4.69E-06