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 mr1281 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
vg0220806690 sf0220800822 2 20806690 2.93E-14 NA
vg1205699586 sf1205698568 12 5699586 8.48E-14 NA
vg0321088836 sf0321087346 3 21088836 1.44E-13 NA
vg1110112955 sf1110107532 11 10112955 2.25E-13 NA
vg0714933670 sf0714932677 7 14933670 3.01E-13 NA
vg0217616831 sf0217610961 2 17616831 2.21E-12 NA
vg0725312603 sf0725311609 7 25312603 9.48E-11 2.17E-06
vg0330420931 sf0330413820 3 30420931 1.19E-10 3.83E-06
vg1106746957 sf1106742710 11 6746957 NA 1.88E-07
vg0211330175 sf0211330172 2 11330175 NA 1.34E-06
vg0724505923 sf0724504929 7 24505923 NA 2.16E-06
vg0804915302 sf0804914305 8 4915302 NA 2.22E-06
vg0710331329 sf0710330335 7 10331329 NA 4.80E-06