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 mr1350 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
vg0413703707 sf0413694421 4 13703707 3.28E-15 1.28E-12
vg0413703292 sf0413694006 4 13703292 6.52E-15 8.01E-13
vg1215444338 sf1215441636 12 15444338 2.79E-11 6.06E-09
vg0311866840 sf0311865558 3 11866840 3.40E-11 NA
vg0801867232 sf0801866235 8 1867232 3.55E-11 NA
vg0704371633 sf0704370634 7 4371633 7.59E-11 2.15E-07
vg1215445580 sf1215442878 12 15445580 1.92E-10 6.11E-10
vg1204271026 sf1204270014 12 4271026 2.65E-10 9.59E-08
vg0310649505 sf0310648421 3 10649505 3.47E-10 6.08E-07
vg1205373977 sf1205372963 12 5373977 6.82E-10 5.21E-08
vg0904766722 sf0904765722 9 4766722 9.16E-10 1.35E-07
vg0905973876 sf0905972876 9 5973876 1.85E-09 7.07E-07
vg1213226496 sf1213223834 12 13226496 2.53E-09 1.29E-06
vg1119011995 sf1118545683 11 19011995 2.62E-09 6.27E-08
vg1011443444 sf1011372263 10 11443444 2.83E-09 2.01E-07
vg1127224190 sf1126752577 11 27224190 5.82E-09 1.95E-08
vg1208230184 sf1208227589 12 8230184 1.64E-08 1.28E-07
vg0723902655 sf0723901661 7 23902655 1.98E-08 1.77E-06
vg0130692417 sf0130691373 1 30692417 2.31E-08 1.47E-06
vg1108160327 sf1108156072 11 8160327 2.47E-08 5.27E-07
vg0334095562 sf0334088432 3 34095562 5.77E-08 5.53E-07
vg0208199705 sf0208199704 2 8199705 5.88E-08 NA
vg0609745094 sf0609744095 6 9745094 9.44E-08 3.48E-07
vg0709622923 sf0709621929 7 9622923 NA 1.22E-06
vg1219583736 sf1219555206 12 19583736 NA 1.58E-06
vg1209262955 sf1209260364 12 9262955 NA 6.22E-06