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 mr1218 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
vg0610587852 sf0610586853 6 10587852 3.07E-37 2.18E-18
vg0610645680 sf0610644681 6 10645680 4.13E-25 6.91E-14
vg0617155455 sf0617154458 6 17155455 2.82E-22 1.54E-06
vg0629122299 sf0629121301 6 29122299 5.66E-19 NA
vg0627151716 sf0627150719 6 27151716 2.92E-18 NA
vg0613725364 sf0613724365 6 13725364 5.68E-18 NA
vg0318752571 sf0318751331 3 18752571 6.80E-15 NA
vg1103952942 sf1103948844 11 3952942 2.53E-14 3.79E-06
vg0610787522 sf0610786523 6 10787522 NA 2.27E-09
vg0610013202 sf0610012203 6 10013202 NA 1.78E-08
vg0610596670 sf0610595671 6 10596670 NA 1.50E-07
vg0610028912 sf0610027913 6 10028912 NA 3.31E-07
vg0610636368 sf0610635369 6 10636368 NA 4.09E-07
vg1102378831 sf1102374690 11 2378831 NA 6.21E-07
vg0610912643 sf0610911644 6 10912643 NA 1.17E-06
vg0610848809 sf0610847810 6 10848809 NA 1.38E-06
vg0610183548 sf0610182549 6 10183548 NA 1.49E-06
vg1017311370 sf1017240143 10 17311370 NA 2.03E-06
vg0611912637 sf0611911638 6 11912637 NA 2.33E-06
vg0320733462 sf0320731972 3 20733462 NA 2.36E-06
vg0719457334 sf0719456341 7 19457334 NA 8.27E-06