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 mr1831 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
vg0223518528 sf0223512659 2 23518528 2.14E-08 NA
vg0132005816 sf0132004772 1 32005816 4.42E-08 9.49E-06
vg0517975909 sf0517915395 5 17975909 7.42E-08 1.43E-06
vg0607961607 sf0607960608 6 7961607 9.29E-08 1.41E-06
vg0102103204 sf0102102204 1 2103204 1.19E-07 1.57E-06
vg0303457724 sf0303456720 3 3457724 1.34E-06 2.86E-06
vg0203000556 sf0203000554 2 3000556 5.55E-06 1.26E-06
vg0915815139 sf0915814138 9 15815139 NA 6.18E-07
vg0408147564 sf0408142838 4 8147564 NA 4.94E-06