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 mr1389 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
vg0728442720 sf0728441728 7 28442720 5.01E-34 3.24E-20
vg0631155509 sf0631154511 6 31155509 1.13E-22 1.60E-10
vg1222591917 sf1222558356 12 22591917 2.34E-22 3.87E-14
vg0422607855 sf0422422737 4 22607855 4.97E-21 1.01E-06
vg0330661173 sf0330654060 3 30661173 8.47E-21 8.34E-06
vg0219834070 sf0219828202 2 19834070 2.05E-20 1.98E-11
vg0431097967 sf0430912856 4 31097967 2.50E-20 1.09E-08
vg0728693760 sf0728692768 7 28693760 3.26E-20 2.03E-15
vg0330452376 sf0330445265 3 30452376 3.15E-19 4.05E-11
vg0202925463 sf0202925461 2 2925463 1.98E-18 1.14E-11
vg1201066168 sf1201065168 12 1066168 2.65E-17 2.72E-09
vg0622846135 sf0622845138 6 22846135 7.82E-17 7.81E-10
vg0325722534 sf0325720552 3 25722534 1.39E-15 2.43E-08
vg1206967731 sf1206966621 12 6967731 1.86E-14 1.64E-10
vg0526514954 sf0526452318 5 26514954 9.54E-14 2.34E-09
vg1219449222 sf1219420692 12 19449222 9.89E-13 6.22E-09
vg0224908970 sf0224903101 2 24908970 1.05E-12 1.15E-08
vg0418804402 sf0418632447 4 18804402 1.11E-12 1.57E-09
vg0418857060 sf0418685104 4 18857060 7.74E-11 3.61E-08
vg0729416948 sf0729415956 7 29416948 2.98E-10 8.49E-08
vg0418822416 sf0418650459 4 18822416 8.26E-09 NA
vg0406740172 sf0406735618 4 6740172 2.02E-08 7.72E-09
vg1215746295 sf1215743592 12 15746295 2.11E-08 9.81E-09
vg0706643852 sf0706642857 7 6643852 1.65E-07 1.01E-08
vg1101299110 sf1101298111 11 1299110 NA 2.42E-08
vg0919476706 sf0919476296 9 19476706 NA 1.20E-07