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 mr1334 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
vg1220775425 sf1220741973 12 20775425 4.40E-195 1.73E-67
vg1220404630 sf1220376072 12 20404630 4.45E-194 7.04E-69
vg1220731451 sf1220697999 12 20731451 2.98E-190 9.21E-69
vg1217257899 sf1217251854 12 17257899 5.03E-128 7.00E-14
vg0128519132 sf0128518087 1 28519132 3.39E-120 7.20E-08
vg0128496460 sf0128495415 1 28496460 3.01E-117 1.25E-09
vg0805415602 sf0805414605 8 5415602 7.36E-114 3.98E-06
vg0132756853 sf0132755809 1 32756853 1.64E-111 NA
vg1224719973 sf1224686427 12 24719973 2.54E-109 4.11E-13
vg0216738012 sf0216732142 2 16738012 2.80E-97 2.42E-07
vg0124627216 sf0124626172 1 24627216 4.27E-96 5.09E-09
vg1220173627 sf1220145069 12 20173627 NA 2.30E-16
vg1220773854 sf1220740402 12 20773854 NA 6.02E-15
vg1220380598 sf1220352040 12 20380598 NA 1.66E-14
vg1220093634 sf1220065076 12 20093634 NA 2.57E-14
vg0223104206 sf0223098337 2 23104206 NA 1.54E-12
vg0807262913 sf0807261918 8 7262913 NA 1.55E-10
vg1220011842 sf1219983284 12 20011842 NA 2.29E-09
vg1220174021 sf1220145463 12 20174021 NA 3.32E-09
vg0304041965 sf0304040961 3 4041965 NA 4.32E-09
vg0114831954 sf0114830928 1 14831954 NA 5.17E-09
vg1221092868 sf1221059418 12 21092868 NA 6.52E-09
vg1217002530 sf1216996484 12 17002530 NA 7.22E-09
vg1220407459 sf1220378901 12 20407459 NA 1.37E-08
vg1220186069 sf1220157511 12 20186069 NA 1.45E-08
vg0211277323 sf0211277320 2 11277323 NA 2.27E-08
vg0222145571 sf0222139702 2 22145571 NA 8.29E-08
vg0223615815 sf0223609946 2 23615815 NA 1.68E-07