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 mr1599 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
vg0216822884 sf0216817014 2 16822884 1.31E-70 9.44E-28
vg0216057693 sf0216051823 2 16057693 1.62E-65 1.60E-10
vg0216699507 sf0216693637 2 16699507 1.79E-65 3.87E-13
vg0216721532 sf0216715662 2 16721532 1.63E-61 4.19E-13
vg0720349785 sf0720348792 7 20349785 1.86E-58 NA
vg1100954914 sf1100953915 11 954914 2.66E-56 NA
vg0310273738 sf0310272654 3 10273738 1.11E-55 NA
vg0206372400 sf0206372400 2 6372400 6.33E-51 2.16E-06
vg0217137734 sf0217131864 2 17137734 NA 4.53E-14
vg0214316674 sf0214310804 2 14316674 NA 1.13E-10
vg0216773376 sf0216767506 2 16773376 NA 4.03E-09
vg0812023942 sf0812022947 8 12023942 NA 7.86E-09
vg1114473442 sf1114009759 11 14473442 NA 1.02E-08
vg1005364262 sf1005380799 10 5364262 NA 4.26E-08
vg1105770829 sf1105766581 11 5770829 NA 9.32E-08
vg0900336799 sf0900335799 9 336799 NA 1.58E-07
vg0525983334 sf0525920754 5 25983334 NA 2.98E-07
vg0631235279 sf0631234281 6 31235279 NA 3.09E-07
vg1112889066 sf1112425387 11 12889066 NA 5.16E-07
vg0519673741 sf0519611225 5 19673741 NA 1.25E-06
vg0217270732 sf0217264862 2 17270732 NA 1.68E-06
vg0217051176 sf0217045306 2 17051176 NA 3.67E-06
vg0211725986 sf0211725982 2 11725986 NA 3.78E-06
vg0220482078 sf0220476210 2 20482078 NA 4.64E-06
vg1105269968 sf1105265719 11 5269968 NA 8.70E-06