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 mr1130 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
vg0222719604 sf0222713735 2 22719604 1.27E-31 8.45E-22
vg0222726032 sf0222720163 2 22726032 3.91E-31 1.84E-22
vg0223077967 sf0223072098 2 23077967 5.31E-12 5.90E-08
vg0224107167 sf0224101298 2 24107167 1.23E-11 3.52E-06
vg0224107309 sf0224101440 2 24107309 1.28E-11 1.39E-06
vg0321808235 sf0321806745 3 21808235 2.75E-11 NA
vg1102212062 sf1102207920 11 2212062 4.47E-11 NA
vg0222799001 sf0222793132 2 22799001 3.22E-08 3.11E-06
vg0224129317 sf0224123448 2 24129317 5.30E-08 1.53E-06
vg0405180721 sf0405176163 4 5180721 5.02E-07 NA
vg0222624829 sf0222618960 2 22624829 7.40E-07 3.82E-07
vg0428798409 sf0428613259 4 28798409 3.10E-06 1.50E-06
vg0525239875 sf0525177296 5 25239875 NA 2.83E-06