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 mr1244 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 2.32E-51 1.67E-12
vg0610584513 sf0610583514 6 10584513 1.84E-48 2.28E-15
vg0402394158 sf0402389753 4 2394158 1.38E-33 NA
vg0719259692 sf0719258699 7 19259692 5.17E-33 NA
vg0228581225 sf0228575356 2 28581225 1.23E-31 NA
vg0122081052 sf0122080007 1 22081052 1.84E-31 NA
vg0520080128 sf0520017604 5 20080128 3.48E-26 2.36E-07
vg0818237210 sf0818234497 8 18237210 9.13E-26 7.96E-08
vg0331908904 sf0331901781 3 31908904 6.13E-25 1.73E-07
vg0221672771 sf0221666902 2 21672771 8.52E-25 4.43E-08
vg0506372331 sf0506372270 5 6372331 1.91E-24 6.04E-09
vg0610553003 sf0610552004 6 10553003 NA 2.28E-10
vg0920309427 sf0920308946 9 20309427 NA 2.72E-09
vg1208012200 sf1208009606 12 8012200 NA 3.45E-09
vg0920306905 sf0920306424 9 20306905 NA 4.32E-09
vg1208012170 sf1208009576 12 8012170 NA 4.68E-09
vg0609655595 sf0609654596 6 9655595 NA 9.05E-09
vg0609873767 sf0609872768 6 9873767 NA 9.93E-09
vg0610532672 sf0610531673 6 10532672 NA 5.07E-08
vg1012246009 sf1012174824 10 12246009 NA 1.67E-07
vg1207996803 sf1207994209 12 7996803 NA 1.74E-07
vg0326693812 sf0326686866 3 26693812 NA 1.78E-07
vg0913926334 sf0913925333 9 13926334 NA 3.39E-07
vg0909120210 sf0909119209 9 9120210 NA 4.90E-07
vg0130072231 sf0130071186 1 30072231 NA 5.02E-07
vg1200795879 sf1200794879 12 795879 NA 5.54E-07
vg1007101812 sf1007117435 10 7101812 NA 5.80E-07
vg0130029694 sf0130028649 1 30029694 NA 6.72E-07
vg0130044994 sf0130043949 1 30044994 NA 1.06E-06
vg0517910927 sf0517850413 5 17910927 NA 8.93E-06