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 mr1201 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
vg0605378647 sf0605377648 6 5378647 1.21E-50 9.55E-24
vg0605374097 sf0605373098 6 5374097 1.01E-49 7.69E-23
vg0605311849 sf0605310850 6 5311849 1.35E-49 5.30E-27
vg0605218848 sf0605217849 6 5218848 2.13E-33 4.92E-14
vg0605170851 sf0605169852 6 5170851 9.66E-19 4.07E-09
vg0604859044 sf0604858045 6 4859044 2.17E-18 1.22E-06
vg0605440935 sf0605439936 6 5440935 5.66E-18 6.27E-09
vg0502963065 sf0502963041 5 2963065 1.91E-15 NA
vg0600826406 sf0600825407 6 826406 3.65E-15 NA
vg0604777948 sf0604776949 6 4777948 6.35E-13 6.82E-06
vg0605617450 sf0605616451 6 5617450 NA 1.84E-08
vg0604840270 sf0604839271 6 4840270 NA 8.35E-07
vg0905422573 sf0905421573 9 5422573 NA 3.06E-06