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 mr1100 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
vg0406519287 sf0406514730 4 6519287 2.03E-23 4.45E-17
vg0406389355 sf0406384795 4 6389355 2.88E-21 1.05E-15
vg1017676724 sf1017605497 10 17676724 3.34E-10 9.31E-07
vg0914431217 sf0914430216 9 14431217 7.43E-10 4.13E-06
vg0807117547 sf0807116552 8 7117547 1.45E-09 6.38E-08
vg1122924753 sf1122458624 11 22924753 1.57E-09 1.11E-06
vg1003486707 sf1003485684 10 3486707 2.14E-09 1.30E-07
vg1123064026 sf1122597897 11 23064026 5.06E-09 2.38E-06
vg0324202574 sf0324200653 3 24202574 8.03E-09 4.92E-07
vg0801674326 sf0801673328 8 1674326 4.01E-08 8.74E-07
vg0108612596 sf0108611596 1 8612596 1.09E-07 1.03E-06
vg1209921454 sf1209918864 12 9921454 3.61E-07 6.06E-07
vg0710831430 sf0710830436 7 10831430 3.87E-07 1.01E-06
vg0202518756 sf0202518754 2 2518756 4.09E-07 2.60E-07
vg0333972137 sf0333965007 3 33972137 6.67E-07 NA
vg0521569979 sf0521507420 5 21569979 1.23E-06 1.41E-06
vg0430673937 sf0430488812 4 30673937 3.81E-06 2.80E-06
vg0614107939 sf0614106940 6 14107939 7.85E-06 4.01E-07
vg0101352726 sf0101351726 1 1352726 NA 8.73E-07
vg0114364662 sf0114363636 1 14364662 NA 1.43E-06