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 mr1946 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
vg0310901143 sf0310899861 3 10901143 7.71E-12 NA
vg0721444375 sf0721443382 7 21444375 2.06E-11 NA
vg0125314858 sf0125313814 1 25314858 3.54E-11 NA
vg0608925485 sf0608924486 6 8925485 1.02E-10 NA
vg0412964994 sf0412955705 4 12964994 1.39E-10 NA
vg0406562212 sf0406557655 4 6562212 2.72E-09 4.70E-06
vg0710825207 sf0710824213 7 10825207 2.14E-08 NA
vg0417797862 sf0417625900 4 17797862 3.33E-08 2.51E-06
vg0125172210 sf0125171166 1 25172210 4.31E-08 NA
vg1209489380 sf1209486789 12 9489380 1.17E-07 NA
vg0411783837 sf0411774548 4 11783837 NA 4.57E-07
vg0401600042 sf0401595591 4 1600042 NA 1.89E-06
vg1205351745 sf1205350731 12 5351745 NA 2.19E-06
vg0407810542 sf0407805810 4 7810542 NA 2.67E-06
vg0335755778 sf0335748647 3 35755778 NA 4.74E-06