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 mr1944 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
vg0322119632 sf0322118139 3 22119632 7.19E-39 5.33E-06
vg0212311200 sf0212311196 2 12311200 3.07E-37 NA
vg1119446549 sf1118980237 11 19446549 4.09E-37 NA
vg1218938385 sf1218909820 12 18938385 1.09E-36 NA
vg0205917173 sf0205917173 2 5917173 1.12E-36 NA
vg1218944220 sf1218915655 12 18944220 1.07E-34 NA
vg0526276618 sf0526213982 5 26276618 1.26E-34 2.10E-06
vg0918924003 sf0918923003 9 18924003 NA 6.55E-10
vg0918923523 sf0918922523 9 18923523 NA 3.50E-08
vg0918923865 sf0918922865 9 18923865 NA 5.74E-07
vg0300327473 sf0300326471 3 327473 NA 4.17E-06
vg0208023522 sf0208023521 2 8023522 NA 4.85E-06