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 mr1866 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
vg1215172477 sf1215169813 12 15172477 8.38E-15 4.53E-06
vg0301928184 sf0301927180 3 1928184 1.12E-12 1.37E-06
vg0113576686 sf0113575660 1 13576686 3.03E-12 NA
vg1005170915 sf1005187452 10 5170915 3.21E-12 NA
vg1216560726 sf1216558019 12 16560726 3.95E-12 NA
vg1218169348 sf1218140784 12 18169348 1.19E-11 3.97E-06
vg1218087228 sf1218058664 12 18087228 5.08E-11 NA
vg1218161842 sf1218133278 12 18161842 6.65E-10 2.24E-06
vg1112861978 sf1112398299 11 12861978 2.60E-09 NA
vg0406886096 sf0406881355 4 6886096 3.00E-09 5.58E-07
vg0114209037 sf0114208011 1 14209037 6.05E-09 NA
vg0413775660 sf0413766374 4 13775660 NA 2.23E-07
vg0610874578 sf0610873579 6 10874578 NA 6.14E-07
vg0324374395 sf0324372474 3 24374395 NA 9.14E-07
vg0314088295 sf0314086984 3 14088295 NA 1.13E-06
vg0127787157 sf0127786113 1 27787157 NA 1.28E-06
vg1215209953 sf1215207249 12 15209953 NA 3.54E-06
vg1205533524 sf1205532510 12 5533524 NA 3.69E-06