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 mr1075 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
vg0222742146 sf0222736277 2 22742146 1.36E-33 2.16E-20
vg0222745779 sf0222739910 2 22745779 3.84E-33 1.32E-20
vg0223683609 sf0223677740 2 23683609 1.17E-13 3.36E-09
vg1112606104 sf1112142307 11 12606104 3.52E-10 4.93E-06
vg0222477102 sf0222471233 2 22477102 4.07E-10 2.45E-07
vg0224678909 sf0224673040 2 24678909 5.61E-10 NA
vg0225412891 sf0225407022 2 25412891 3.04E-09 1.06E-06
vg0222671915 sf0222666046 2 22671915 1.51E-08 3.09E-09
vg0809657271 sf0809656275 8 9657271 2.88E-08 3.31E-06
vg0222620162 sf0222614293 2 22620162 5.37E-08 4.52E-06
vg0613063818 sf0613062819 6 13063818 2.92E-07 NA
vg0904658178 sf0904657178 9 4658178 3.00E-07 3.95E-07
vg1017015778 sf1016944550 10 17015778 8.12E-07 1.82E-06
vg0715115605 sf0715114612 7 15115605 NA 1.60E-07
vg0922300827 sf0922300346 9 22300827 NA 4.40E-06