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 mr1068 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
vg0610566084 sf0610565085 6 10566084 4.54E-81 7.00E-54
vg0610873460 sf0610872461 6 10873460 9.10E-25 8.04E-15
vg0610444061 sf0610443062 6 10444061 2.99E-23 1.96E-18
vg0611098730 sf0611097731 6 11098730 6.18E-23 2.55E-16
vg0610679932 sf0610678933 6 10679932 1.04E-22 4.00E-24
vg0610587020 sf0610586021 6 10587020 6.72E-22 8.89E-15
vg0610645250 sf0610644251 6 10645250 2.31E-20 8.16E-13
vg0610435285 sf0610434286 6 10435285 7.26E-20 9.02E-20
vg0611098102 sf0611097103 6 11098102 4.68E-18 1.12E-14
vg0610119475 sf0610118476 6 10119475 1.87E-15 1.39E-16
vg0613057898 sf0613056899 6 13057898 3.73E-15 1.14E-08
vg0610211069 sf0610210070 6 10211069 1.69E-14 1.99E-11
vg0610684751 sf0610683752 6 10684751 2.70E-14 2.32E-08
vg0610428814 sf0610427815 6 10428814 3.47E-14 2.28E-13
vg0617815455 sf0617814458 6 17815455 1.10E-13 3.74E-08
vg0611392640 sf0611391641 6 11392640 1.72E-12 1.63E-10
vg0612015787 sf0612014788 6 12015787 4.20E-12 1.70E-09
vg0610548872 sf0610547873 6 10548872 1.77E-11 2.13E-13
vg0611643367 sf0611642368 6 11643367 1.82E-11 8.86E-12
vg0610532305 sf0610531306 6 10532305 7.07E-11 4.05E-12
vg0613809145 sf0613808146 6 13809145 4.46E-10 5.46E-09
vg0610977106 sf0610976107 6 10977106 1.19E-08 5.17E-11
vg0615048731 sf0615047732 6 15048731 NA 4.49E-10
vg0618988041 sf0618987044 6 18988041 NA 1.44E-09
vg0612328142 sf0612327143 6 12328142 NA 1.80E-08
vg0610772213 sf0610771214 6 10772213 NA 1.83E-07
vg0610801630 sf0610800631 6 10801630 NA 4.75E-06