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 mr1987 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
vg0322632917 sf0322631406 3 22632917 2.61E-175 2.23E-09
vg0321369281 sf0321367791 3 21369281 8.96E-173 7.67E-12
vg0317721273 sf0317720055 3 17721273 5.05E-166 2.58E-09
vg0322099539 sf0322098046 3 22099539 4.92E-162 4.96E-12
vg0215242415 sf0215236545 2 15242415 1.04E-159 NA
vg1227254042 sf1227220442 12 27254042 3.02E-159 NA
vg0327028819 sf0327021872 3 27028819 1.22E-158 NA
vg0215291743 sf0215285873 2 15291743 3.85E-158 1.31E-08
vg0211791834 sf0211791830 2 11791834 NA 3.72E-07
vg0128078191 sf0128077147 1 28078191 NA 7.74E-07
vg0110367769 sf0110366745 1 10367769 NA 8.72E-07
vg1219351662 sf1219323132 12 19351662 NA 9.32E-07
vg0308877969 sf0308876907 3 8877969 NA 1.07E-06
vg0620696591 sf0620695594 6 20696591 NA 1.58E-06
vg0127793179 sf0127792135 1 27793179 NA 1.93E-06
vg0612806445 sf0612805446 6 12806445 NA 2.33E-06
vg0307974594 sf0307973532 3 7974594 NA 2.49E-06
vg0320914714 sf0320913224 3 20914714 NA 2.71E-06
vg0620381875 sf0620380878 6 20381875 NA 3.44E-06
vg0433026362 sf0432841249 4 33026362 NA 3.82E-06
vg0607359009 sf0607358010 6 7359009 NA 3.91E-06
vg1015985372 sf1015914144 10 15985372 NA 4.85E-06