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 mr1137 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
vg0604305910 sf0604304911 6 4305910 7.21E-34 1.19E-20
vg0604326842 sf0604325843 6 4326842 3.38E-33 1.16E-21
vg0727913447 sf0727912454 7 27913447 9.82E-17 NA
vg0311662859 sf0311661577 3 11662859 4.16E-16 8.95E-06
vg0704817476 sf0704816477 7 4817476 3.58E-15 NA
vg0420495425 sf0420323469 4 20495425 4.86E-15 NA
vg0508706913 sf0508706841 5 8706913 5.00E-15 9.51E-07
vg0609221063 sf0609220064 6 9221063 5.41E-14 2.70E-06
vg0604356746 sf0604355747 6 4356746 9.91E-11 1.72E-11
vg0604550200 sf0604549201 6 4550200 NA 3.89E-07
vg0601454762 sf0601453763 6 1454762 NA 2.32E-06
vg1119833937 sf1119370388 11 19833937 NA 4.51E-06