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 mr1929 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
vg0222739831 sf0222733962 2 22739831 2.17E-38 1.04E-36
vg0223639121 sf0223633252 2 23639121 2.44E-09 1.87E-08
vg0222615084 sf0222609215 2 22615084 6.18E-09 8.44E-07
vg0222743406 sf0222737537 2 22743406 8.50E-09 6.15E-08
vg0223030002 sf0223024133 2 23030002 1.52E-08 NA
vg0222729132 sf0222723263 2 22729132 1.61E-08 8.99E-07
vg0222765370 sf0222759501 2 22765370 3.00E-08 2.93E-06
vg0222879623 sf0222873754 2 22879623 5.16E-08 3.40E-09
vg0223049822 sf0223043953 2 23049822 6.17E-08 4.31E-09
vg0221650044 sf0221644175 2 21650044 2.33E-07 8.51E-07
vg0222799001 sf0222793132 2 22799001 5.17E-07 2.70E-06
vg0224233108 sf0224227239 2 24233108 1.15E-06 2.60E-06
vg1112606022 sf1112142225 11 12606022 1.86E-06 1.11E-06
vg0610639681 sf0610638682 6 10639681 3.13E-06 8.07E-07
vg0223039697 sf0223033828 2 23039697 3.66E-06 1.59E-07
vg0612532192 sf0612531193 6 12532192 NA 1.62E-06
vg0222652666 sf0222646797 2 22652666 NA 2.42E-06
vg0711810587 sf0711809593 7 11810587 NA 4.72E-06