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 mr1098 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
vg0221025908 sf0221020040 2 21025908 3.76E-09 1.89E-08
vg0727090466 sf0727089472 7 27090466 6.10E-09 5.13E-08
vg0402179876 sf0402175471 4 2179876 3.22E-08 9.72E-06
vg0904766722 sf0904765722 9 4766722 6.42E-08 NA
vg0222833455 sf0222827586 2 22833455 7.48E-08 4.78E-07
vg0628759426 sf0628758428 6 28759426 1.02E-07 3.65E-06
vg0819421680 sf0819418967 8 19421680 1.22E-07 1.71E-06
vg0207643505 sf0207643505 2 7643505 4.04E-07 2.80E-06
vg0808077570 sf0808076574 8 8077570 5.45E-07 2.51E-06
vg0906540051 sf0906539051 9 6540051 8.20E-07 4.08E-06
vg1221097233 sf1221063783 12 21097233 8.92E-07 5.07E-07
vg0920644583 sf0920644102 9 20644583 1.73E-06 4.01E-07
vg0208050121 sf0208050120 2 8050121 6.48E-06 3.29E-06
vg0901498790 sf0901497790 9 1498790 NA 8.18E-07
vg1005855806 sf1005872344 10 5855806 NA 1.31E-06
vg0919581492 sf0919581082 9 19581492 NA 2.30E-06
vg1214613948 sf1214611288 12 14613948 NA 3.27E-06
vg1118461468 sf1117995327 11 18461468 NA 4.48E-06