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 mr1221 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
vg0610596040 sf0610595041 6 10596040 5.59E-27 4.48E-17
vg0629122924 sf0629121926 6 29122924 8.62E-14 9.64E-08
vg0610457875 sf0610456876 6 10457875 9.33E-13 1.99E-10
vg0610365502 sf0610364503 6 10365502 1.68E-12 2.96E-09
vg0610363971 sf0610362972 6 10363971 4.16E-12 7.91E-09
vg0610674308 sf0610673309 6 10674308 8.17E-11 6.01E-10
vg0617359224 sf0617358227 6 17359224 1.64E-10 NA
vg0612015351 sf0612014352 6 12015351 5.99E-10 7.32E-07
vg0610884530 sf0610883531 6 10884530 1.07E-09 2.41E-06
vg0611584863 sf0611583864 6 11584863 4.04E-09 5.96E-07
vg0610135843 sf0610134844 6 10135843 1.73E-08 2.85E-06
vg0321989245 sf0321987752 3 21989245 2.80E-08 4.08E-06
vg0319208851 sf0319207611 3 19208851 6.76E-08 NA
vg0905154807 sf0905153807 9 5154807 5.00E-07 NA
vg0610974808 sf0610973809 6 10974808 5.68E-07 1.55E-06
vg0611342932 sf0611341933 6 11342932 NA 3.40E-06