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 mr1662 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
vg1125500282 sf1125034121 11 25500282 8.33E-34 2.54E-25
vg1125514201 sf1125048040 11 25514201 9.20E-21 4.36E-17
vg1125443202 sf1124977041 11 25443202 1.69E-20 2.43E-14
vg1125471656 sf1125005495 11 25471656 1.91E-16 1.78E-15
vg1125473544 sf1125007383 11 25473544 6.93E-16 3.89E-14
vg1126612499 sf1126140914 11 26612499 2.00E-14 9.26E-08
vg1125425266 sf1124959105 11 25425266 4.78E-14 3.43E-12
vg1125175150 sf1124708990 11 25175150 5.69E-14 3.53E-09
vg1125557272 sf1125091111 11 25557272 4.92E-13 9.89E-08
vg1125185237 sf1124719077 11 25185237 2.26E-12 3.33E-19
vg1122457949 sf1121991820 11 22457949 3.49E-12 5.48E-09
vg0507714473 sf0507714414 5 7714473 9.94E-11 6.48E-08
vg1125369517 sf1124903357 11 25369517 3.45E-10 1.38E-07
vg0713263559 sf0713262566 7 13263559 4.38E-10 3.35E-07
vg1126423874 sf1125952287 11 26423874 1.47E-09 2.17E-07
vg1125609366 sf1125143205 11 25609366 3.23E-09 1.20E-07
vg1125225529 sf1124759369 11 25225529 4.93E-09 8.34E-09
vg1126586105 sf1126114520 11 26586105 9.32E-09 3.30E-07
vg1125231256 sf1124765096 11 25231256 9.08E-08 1.28E-11
vg1128476692 sf1127953471 11 28476692 3.44E-07 3.58E-07
vg1125468295 sf1125002134 11 25468295 3.68E-07 5.24E-11
vg1125819702 sf1125353623 11 25819702 8.83E-07 4.69E-07
vg1125530448 sf1125064287 11 25530448 9.47E-07 2.23E-07