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 mr1164 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
vg0133085251 sf0133084207 1 33085251 1.77E-30 4.84E-06
vg0229153698 sf0229147829 2 29153698 1.49E-28 2.28E-06
vg0202240863 sf0202240863 2 2240863 2.07E-27 6.59E-08
vg0435366429 sf0435181311 4 35366429 9.05E-27 NA
vg0917567303 sf0917566302 9 17567303 1.17E-26 NA
vg0112172810 sf0112171784 1 12172810 6.25E-26 4.64E-06
vg0124418254 sf0124417210 1 24418254 7.56E-26 4.80E-09
vg1225227350 sf1225193748 12 25227350 1.71E-24 NA
vg0131033386 sf0131032342 1 31033386 1.11E-23 1.51E-06
vg0434493414 sf0434308307 4 34493414 1.80E-22 3.55E-06
vg0140815392 sf0140814349 1 40815392 5.30E-21 3.55E-07
vg0910406964 sf0910405963 9 10406964 1.32E-20 2.38E-06
vg0425921230 sf0425736105 4 25921230 NA 4.16E-09
vg0135821566 sf0135820523 1 35821566 NA 2.60E-08
vg1210724034 sf1210721447 12 10724034 NA 4.18E-08
vg0112928822 sf0112927796 1 12928822 NA 1.21E-07
vg0112034045 sf0112033019 1 12034045 NA 3.63E-07
vg0602041882 sf0602040883 6 2041882 NA 3.94E-07
vg0124416834 sf0124415790 1 24416834 NA 5.94E-07
vg1203618566 sf1203617565 12 3618566 NA 6.40E-07
vg1210774599 sf1210771965 12 10774599 NA 1.05E-06
vg0506138324 sf0506138263 5 6138324 NA 1.26E-06
vg0303001255 sf0303000251 3 3001255 NA 2.20E-06
vg0303425859 sf0303424855 3 3425859 NA 2.82E-06
vg0124465856 sf0124464812 1 24465856 NA 3.22E-06
vg0119052418 sf0119051373 1 19052418 NA 3.36E-06
vg0227924870 sf0227919001 2 27924870 NA 3.70E-06