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 mr1816 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
vg0819603039 sf0819600326 8 19603039 3.60E-08 3.60E-08
vg0122971925 sf0122970881 1 22971925 1.23E-07 1.23E-07
vg0122971893 sf0122970849 1 22971893 2.38E-07 2.39E-07
vg0420711795 sf0420539838 4 20711795 8.79E-07 8.79E-07
vg0717084739 sf0717083746 7 17084739 1.17E-06 1.17E-06
vg0607674962 sf0607673963 6 7674962 1.47E-06 1.47E-06
vg0131779655 sf0131778611 1 31779655 1.60E-06 1.60E-06
vg0921004343 sf0921003862 9 21004343 2.44E-06 2.44E-06
vg0527921956 sf0527859313 5 27921956 2.90E-06 2.91E-06
vg0316786845 sf0316785719 3 16786845 3.40E-06 3.40E-06
vg0421220373 sf0421048425 4 21220373 3.42E-06 3.42E-06
vg1215307750 sf1215305048 12 15307750 4.14E-06 4.14E-06
vg0621412586 sf0621411589 6 21412586 4.26E-06 4.26E-06
vg0516508609 sf0516451091 5 16508609 4.39E-06 4.39E-06
vg1012377106 sf1012305921 10 12377106 4.49E-06 4.50E-06
vg0816670160 sf0816667446 8 16670160 4.67E-06 4.67E-06
vg0235581681 sf0235575812 2 35581681 4.80E-06 4.80E-06
vg0102140552 sf0102139552 1 2140552 4.91E-06 4.91E-06