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 mr1448 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
vg0235337136 sf0235331267 2 35337136 5.47E-14 6.00E-11
vg0203671161 sf0203671158 2 3671161 1.38E-11 6.87E-09
vg0914935450 sf0914934449 9 14935450 2.93E-10 2.12E-07
vg0123702220 sf0123701176 1 23702220 3.10E-10 1.22E-07
vg0319082408 sf0319081168 3 19082408 5.14E-10 4.31E-08
vg0523767761 sf0523705182 5 23767761 9.71E-10 1.85E-07
vg0112458126 sf0112457100 1 12458126 1.17E-09 8.44E-08
vg1108660993 sf1108655603 11 8660993 5.35E-09 2.48E-06
vg1114456299 sf1113992616 11 14456299 6.61E-09 5.05E-07
vg1208599063 sf1208596470 12 8599063 8.38E-09 8.05E-07
vg0143123163 sf0143122119 1 43123163 1.63E-08 3.26E-06
vg0416678412 sf0416506455 4 16678412 3.74E-08 4.31E-06
vg0802877898 sf0802876901 8 2877898 4.80E-08 4.91E-06
vg0112192551 sf0112191525 1 12192551 2.37E-07 1.88E-06
vg0235318648 sf0235312779 2 35318648 NA 1.94E-06
vg0808663281 sf0808662285 8 8663281 NA 4.55E-06