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 mr1379 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
vg0216741216 sf0216735346 2 16741216 1.16E-22 6.28E-12
vg0217146199 sf0217140329 2 17146199 1.02E-20 1.22E-09
vg0216616099 sf0216610229 2 16616099 5.83E-19 2.40E-10
vg0216745313 sf0216739443 2 16745313 1.80E-17 2.31E-12
vg1004020304 sf1004019280 10 4020304 2.05E-14 NA
vg0210216171 sf0210216169 2 10216171 2.21E-14 NA
vg0228175413 sf0228169544 2 28175413 8.24E-14 4.41E-07
vg0206037285 sf0206037285 2 6037285 1.30E-13 3.13E-06
vg0715704106 sf0715703113 7 15704106 4.81E-12 NA
vg0217258529 sf0217252659 2 17258529 6.58E-10 8.10E-08
vg0216629794 sf0216623924 2 16629794 NA 2.59E-07
vg0430616892 sf0430431767 4 30616892 NA 1.10E-06
vg0137962179 sf0137961136 1 37962179 NA 1.58E-06
vg0323687205 sf0323685379 3 23687205 NA 2.75E-06
vg0324795678 sf0324793757 3 24795678 NA 4.03E-06
vg0133452014 sf0133450970 1 33452014 NA 4.95E-06