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 mr1563 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
vg0723332364 sf0723331371 7 23332364 7.04E-137 1.13E-54
vg0723322944 sf0723321951 7 23322944 2.63E-136 1.94E-58
vg0802395099 sf0802394102 8 2395099 1.08E-92 1.43E-07
vg0137168967 sf0137167924 1 37168967 1.25E-87 NA
vg0626826434 sf0626825437 6 26826434 5.26E-87 7.99E-06
vg0309857600 sf0309856536 3 9857600 1.23E-84 NA
vg0720357187 sf0720356194 7 20357187 3.04E-79 1.89E-07
vg0723355917 sf0723354924 7 23355917 NA 1.53E-23
vg0723323149 sf0723322156 7 23323149 NA 1.21E-18
vg0818069929 sf0818067216 8 18069929 NA 2.07E-08
vg1219210664 sf1219182134 12 19210664 NA 2.29E-08
vg0221725390 sf0221719521 2 21725390 NA 3.97E-08
vg0402757872 sf0402753477 4 2757872 NA 6.28E-08
vg0709565998 sf0709565004 7 9565998 NA 8.23E-08
vg0724694165 sf0724693171 7 24694165 NA 1.02E-07
vg0917104627 sf0917103626 9 17104627 NA 1.22E-07
vg0720354763 sf0720353770 7 20354763 NA 1.42E-07
vg0725341223 sf0725340229 7 25341223 NA 2.09E-07
vg0400212499 sf0400211499 4 212499 NA 2.41E-07
vg0206815673 sf0206815673 2 6815673 NA 3.75E-07
vg0820921834 sf0820919121 8 20921834 NA 3.80E-07
vg0917104147 sf0917103146 9 17104147 NA 4.66E-07
vg0206930782 sf0206930782 2 6930782 NA 7.07E-07
vg1004001379 sf1004000355 10 4001379 NA 8.95E-07
vg0704728125 sf0704727126 7 4728125 NA 1.19E-06
vg0405036104 sf0405031543 4 5036104 NA 1.27E-06
vg0106216371 sf0106215371 1 6216371 NA 2.16E-06
vg0820968196 sf0820965483 8 20968196 NA 2.60E-06
vg0807743041 sf0807742045 8 7743041 NA 2.63E-06
vg1004639213 sf1004655750 10 4639213 NA 5.92E-06