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 mr1927 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
vg0217095683 sf0217089813 2 17095683 8.04E-51 1.45E-28
vg0216789715 sf0216783845 2 16789715 2.49E-50 1.06E-28
vg1108225523 sf1108220133 11 8225523 4.35E-21 4.10E-06
vg1220336317 sf1220307759 12 20336317 2.79E-20 8.33E-07
vg1220336354 sf1220307796 12 20336354 3.10E-20 7.12E-07
vg1128516527 sf1127993306 11 28516527 1.66E-18 NA
vg0217555934 sf0217550064 2 17555934 3.53E-17 3.01E-08
vg0218856450 sf0218850581 2 18856450 4.25E-16 3.05E-06
vg1216728542 sf1216722496 12 16728542 2.90E-15 1.09E-06
vg0216424953 sf0216419083 2 16424953 2.15E-13 6.41E-08
vg0422159758 sf0421974639 4 22159758 6.52E-09 4.23E-06
vg0216627913 sf0216622043 2 16627913 6.44E-08 5.58E-08
vg0514271389 sf0514213932 5 14271389 NA 4.59E-06
vg0427400029 sf0427214893 4 27400029 NA 4.71E-06