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 mr1892 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
vg0336109020 sf0336101946 3 36109020 1.70E-10 8.54E-09
vg0123807604 sf0123806560 1 23807604 7.30E-10 NA
vg1125228741 sf1124762581 11 25228741 1.25E-09 5.96E-07
vg0122421655 sf0122420610 1 22421655 2.36E-09 1.26E-06
vg0128527221 sf0128526176 1 28527221 5.17E-09 NA
vg0336089219 sf0336082145 3 36089219 1.33E-07 2.92E-06
vg0630856304 sf0630855306 6 30856304 8.28E-07 NA
vg0141987444 sf0141986401 1 41987444 2.15E-06 NA
vg0803221452 sf0803220455 8 3221452 5.33E-06 1.66E-06
vg1210199420 sf1210196831 12 10199420 NA 3.29E-06