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 mr1222 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
vg0222732157 sf0222726288 2 22732157 2.75E-48 3.11E-37
vg0222725003 sf0222719134 2 22725003 1.05E-22 1.28E-16
vg0223908663 sf0223902794 2 23908663 2.17E-15 1.52E-06
vg0122744244 sf0122743200 1 22744244 5.59E-15 NA
vg0601461905 sf0601460906 6 1461905 7.70E-13 NA
vg0223169891 sf0223164022 2 23169891 4.43E-11 3.21E-07
vg0222857256 sf0222851387 2 22857256 8.33E-11 3.67E-07
vg0713287889 sf0713286896 7 13287889 4.93E-10 2.54E-06
vg0224832469 sf0224826600 2 24832469 2.68E-09 2.77E-06
vg0222817468 sf0222811599 2 22817468 NA 6.49E-10
vg0224664402 sf0224658533 2 24664402 NA 4.82E-09
vg0225441549 sf0225435680 2 25441549 NA 4.75E-07
vg0225439704 sf0225433835 2 25439704 NA 7.17E-07
vg0610462536 sf0610461537 6 10462536 NA 1.30E-06
vg0223688130 sf0223682261 2 23688130 NA 1.31E-06
vg0335727001 sf0335719870 3 35727001 NA 1.99E-06