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 mr1162 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
vg0314130207 sf0314128896 3 14130207 6.52E-19 NA
vg0524611484 sf0524548904 5 24611484 7.64E-19 NA
vg0529371849 sf0529309204 5 29371849 2.44E-18 NA
vg0114594007 sf0114592981 1 14594007 3.12E-18 NA
vg0809308950 sf0809307954 8 9308950 5.24E-18 NA
vg0328245483 sf0328238537 3 28245483 4.81E-17 NA
vg1216564044 sf1216561337 12 16564044 1.03E-16 3.09E-06
vg1216580086 sf1216577379 12 16580086 2.18E-15 5.11E-06
vg0620976126 sf0620975129 6 20976126 NA 6.63E-07
vg0122938954 sf0122937910 1 22938954 NA 2.71E-06
vg1106573600 sf1106569353 11 6573600 NA 3.48E-06
vg1208635661 sf1208633068 12 8635661 NA 3.77E-06