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 mr1873 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
vg0506861028 sf0506860970 5 6861028 4.13E-44 1.75E-10
vg0506933059 sf0506933001 5 6933059 1.76E-43 1.49E-11
vg0514708030 sf0514650573 5 14708030 3.69E-40 8.23E-10
vg0514650910 sf0514593453 5 14650910 1.43E-39 3.65E-10
vg0427858791 sf0427673653 4 27858791 4.04E-39 8.27E-08
vg0916156955 sf0916155954 9 16156955 8.32E-38 NA
vg0922013395 sf0922012914 9 22013395 7.36E-37 NA
vg0506835240 sf0506835182 5 6835240 NA 1.53E-11
vg0432523577 sf0432338469 4 32523577 NA 1.65E-09
vg0428450149 sf0428265002 4 28450149 NA 4.93E-07
vg0117519898 sf0117518852 1 17519898 NA 5.04E-07
vg0322560129 sf0322558618 3 22560129 NA 8.90E-07
vg0426557459 sf0426372332 4 26557459 NA 1.94E-06
vg0432657154 sf0432472043 4 32657154 NA 3.68E-06
vg0514865114 sf0514807657 5 14865114 NA 4.58E-06