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 mr1219 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
vg0605274340 sf0605273341 6 5274340 8.20E-39 8.48E-24
vg0605332135 sf0605331136 6 5332135 4.78E-29 5.62E-16
vg0605306584 sf0605305585 6 5306584 8.60E-16 8.69E-14
vg0605105760 sf0605104761 6 5105760 9.88E-16 6.03E-10
vg0605049951 sf0605048952 6 5049951 1.04E-15 6.52E-11
vg0605270755 sf0605269756 6 5270755 1.02E-14 5.48E-08
vg0605448742 sf0605447743 6 5448742 4.13E-14 9.51E-08
vg0605433695 sf0605432696 6 5433695 4.32E-14 2.39E-08
vg0605311849 sf0605310850 6 5311849 6.49E-14 8.99E-18
vg0209219211 sf0209219209 2 9219211 3.02E-09 3.46E-06
vg0803676578 sf0803675581 8 3676578 3.71E-08 1.56E-06
vg0507593806 sf0507593747 5 7593806 1.14E-07 4.49E-06
vg0605321614 sf0605320615 6 5321614 3.66E-07 6.04E-09
vg0200067614 sf0200067614 2 67614 6.13E-07 1.57E-08
vg1001118141 sf1001117117 10 1118141 6.17E-06 NA
vg0605259601 sf0605258602 6 5259601 NA 4.14E-09
vg0125383093 sf0125382049 1 25383093 NA 9.68E-08
vg0920825892 sf0920825411 9 20825892 NA 2.50E-07
vg0125462906 sf0125461862 1 25462906 NA 4.21E-07
vg0431357155 sf0431172049 4 31357155 NA 4.87E-07
vg0605343435 sf0605342436 6 5343435 NA 1.74E-06
vg1204986534 sf1204985520 12 4986534 NA 2.49E-06
vg0207302554 sf0207302554 2 7302554 NA 2.56E-06
vg0127396120 sf0127395076 1 27396120 NA 3.37E-06