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 mr1936 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
vg0222889740 sf0222883871 2 22889740 4.31E-33 1.24E-15
vg0222735698 sf0222729829 2 22735698 8.25E-27 1.42E-10
vg0611741443 sf0611740444 6 11741443 1.29E-24 5.04E-06
vg0616934655 sf0616933658 6 16934655 2.83E-24 1.20E-07
vg0624490244 sf0624489247 6 24490244 3.30E-24 3.96E-07
vg0222709250 sf0222703381 2 22709250 4.84E-24 3.41E-10
vg0608872938 sf0608871939 6 8872938 6.75E-24 2.83E-06
vg0505989705 sf0505989644 5 5989705 2.67E-23 2.74E-06
vg1110399053 sf1110393598 11 10399053 1.15E-22 4.14E-06
vg0335918912 sf0335911781 3 35918912 8.37E-22 1.51E-07
vg0518621387 sf0518558870 5 18621387 2.58E-21 4.83E-06
vg0316091754 sf0316090401 3 16091754 2.38E-19 4.80E-06
vg1209215198 sf1209212607 12 9215198 1.17E-18 4.03E-06
vg0709983832 sf0709982838 7 9983832 4.02E-18 NA
vg0905697823 sf0905696823 9 5697823 4.87E-18 5.64E-07
vg0327037726 sf0327030779 3 27037726 NA 1.66E-08
vg0819586766 sf0819584053 8 19586766 NA 5.76E-08
vg0626215270 sf0626214273 6 26215270 NA 1.57E-07
vg0129623631 sf0129622586 1 29623631 NA 3.76E-07
vg0232358383 sf0232352514 2 32358383 NA 9.18E-07
vg0220854220 sf0220848352 2 20854220 NA 1.27E-06
vg1016341327 sf1016270103 10 16341327 NA 1.52E-06
vg0434789415 sf0434604306 4 34789415 NA 1.63E-06
vg0222722554 sf0222716685 2 22722554 NA 1.77E-06
vg1009170616 sf1009099437 10 9170616 NA 2.57E-06
vg0709509554 sf0709508560 7 9509554 NA 3.36E-06
vg0220853972 sf0220848104 2 20853972 NA 3.59E-06
vg0133772255 sf0133771211 1 33772255 NA 4.43E-06
vg0107043704 sf0107042704 1 7043704 NA 6.01E-06
vg0503030079 sf0503030055 5 3030079 NA 6.92E-06