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 mr1587 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
vg0314583769 sf0314582456 3 14583769 3.55E-20 8.61E-15
vg1215976850 sf1215974146 12 15976850 4.02E-14 1.22E-06
vg1210580285 sf1210577698 12 10580285 1.80E-12 NA
vg1210654799 sf1210652212 12 10654799 4.09E-12 1.02E-06
vg1216357096 sf1216354392 12 16357096 1.07E-11 3.25E-06
vg1215615147 sf1215612444 12 15615147 3.57E-10 4.95E-07
vg0217094827 sf0217088957 2 17094827 1.10E-09 NA
vg0216743847 sf0216737977 2 16743847 3.81E-09 NA
vg0216799415 sf0216793545 2 16799415 4.65E-08 NA
vg1210023832 sf1210021243 12 10023832 6.33E-08 9.18E-06
vg0314549769 sf0314548457 3 14549769 8.63E-08 4.83E-06
vg0104992072 sf0104991072 1 4992072 3.03E-06 5.79E-07
vg0113853307 sf0113852281 1 13853307 7.47E-06 NA
vg0503508976 sf0503508953 5 3508976 8.90E-06 NA
vg0314514506 sf0314513194 3 14514506 NA 6.92E-08
vg1123957709 sf1123491579 11 23957709 NA 2.63E-06