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 mr1905 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
vg1214822308 sf1214819649 12 14822308 6.07E-08 6.07E-08
vg0217031670 sf0217025800 2 17031670 6.09E-07 6.09E-07
vg0130351635 sf0130350591 1 30351635 1.18E-06 1.18E-06
vg1217707522 sf1217701477 12 17707522 2.16E-06 2.16E-06
vg0103381628 sf0103380628 1 3381628 2.19E-06 2.19E-06
vg0502104489 sf0502104471 5 2104489 3.22E-06 3.22E-06
vg0725376215 sf0725375221 7 25376215 3.70E-06 3.70E-06
vg0213822498 sf0213816628 2 13822498 4.23E-06 4.23E-06