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 mr1657 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
vg1223833401 sf1223799854 12 23833401 1.34E-23 6.41E-07
vg1226205192 sf1226171586 12 26205192 2.80E-23 4.83E-07
vg0104676854 sf0104675854 1 4676854 1.82E-22 NA
vg1223866038 sf1223832491 12 23866038 1.82E-22 3.02E-06
vg1013907854 sf1013836622 10 13907854 2.06E-22 NA
vg0907939520 sf0907938520 9 7939520 3.44E-22 NA
vg0917486570 sf0917485569 9 17486570 4.39E-22 NA
vg0124420361 sf0124419317 1 24420361 1.22E-20 NA
vg1014564871 sf1014493637 10 14564871 4.66E-20 7.44E-07
vg1103076557 sf1103072460 11 3076557 NA 1.14E-06
vg1103068554 sf1103064458 11 3068554 NA 1.90E-06
vg0819105437 sf0819102724 8 19105437 NA 2.04E-06
vg0516563624 sf0516506106 5 16563624 NA 2.09E-06
vg1216110511 sf1216107807 12 16110511 NA 2.36E-06
vg0220305511 sf0220299643 2 20305511 NA 2.60E-06
vg1010728828 sf1010657649 10 10728828 NA 3.22E-06
vg0819985304 sf0819982591 8 19985304 NA 4.68E-06
vg0421366980 sf0421195033 4 21366980 NA 5.27E-06
vg1107108647 sf1107104392 11 7108647 NA 6.79E-06
vg0709199737 sf0709198743 7 9199737 NA 8.55E-06