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 mr1114 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
vg0222687716 sf0222681847 2 22687716 9.63E-51 2.27E-27
vg1110783636 sf1110778181 11 10783636 1.10E-26 9.90E-09
vg0518201525 sf0518141011 5 18201525 8.50E-25 7.77E-07
vg0526722696 sf0526660054 5 26722696 1.29E-24 NA
vg0900825661 sf0900824661 9 825661 1.96E-24 1.04E-07
vg1110750361 sf1110744906 11 10750361 2.03E-24 1.13E-09
vg0818212763 sf0818210050 8 18212763 1.42E-22 1.70E-08
vg0306047262 sf0306046262 3 6047262 5.89E-22 1.66E-08
vg0500664660 sf0500664660 5 664660 1.23E-20 3.58E-08
vg0907026290 sf0907025290 9 7026290 7.61E-20 1.82E-08
vg0716599841 sf0716598848 7 16599841 7.94E-20 9.68E-08
vg1006506535 sf1006522158 10 6506535 4.50E-19 7.47E-07
vg0222722554 sf0222716685 2 22722554 NA 5.34E-11
vg0222952563 sf0222946694 2 22952563 NA 2.16E-09
vg0222700671 sf0222694802 2 22700671 NA 6.02E-09
vg0315713125 sf0315711772 3 15713125 NA 1.15E-08
vg1005950387 sf1005966925 10 5950387 NA 1.81E-08
vg0431376032 sf0431190928 4 31376032 NA 1.86E-08
vg0709372324 sf0709371330 7 9372324 NA 3.70E-08
vg0140883886 sf0140882843 1 40883886 NA 4.17E-08
vg0207115454 sf0207115454 2 7115454 NA 5.02E-08
vg0822600721 sf0822598008 8 22600721 NA 5.23E-08
vg0626215297 sf0626214300 6 26215297 NA 5.52E-08
vg0709837237 sf0709836243 7 9837237 NA 6.04E-08
vg0224791200 sf0224785331 2 24791200 NA 6.36E-08
vg1204507349 sf1204506337 12 4507349 NA 7.20E-08
vg1021149005 sf1021077484 10 21149005 NA 9.38E-08
vg0234022553 sf0234016684 2 34022553 NA 1.77E-07
vg0725440295 sf0725439301 7 25440295 NA 1.19E-06
vg0315922465 sf0315921112 3 15922465 NA 1.98E-06