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 mr1109 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
vg0217033543 sf0217027673 2 17033543 1.62E-50 5.09E-35
vg0812023942 sf0812022947 8 12023942 8.52E-21 1.04E-11
vg0212179963 sf0212179959 2 12179963 4.62E-19 1.81E-10
vg0900337327 sf0900336327 9 337327 6.07E-18 3.33E-09
vg0900336799 sf0900335799 9 336799 6.65E-18 1.86E-09
vg0216448432 sf0216442562 2 16448432 4.46E-16 4.65E-07
vg0216357484 sf0216351614 2 16357484 3.08E-15 4.65E-08
vg1114596727 sf1114133045 11 14596727 3.52E-15 2.22E-06
vg1208648368 sf1208645775 12 8648368 8.55E-14 1.38E-07
vg1005364262 sf1005380799 10 5364262 2.70E-13 8.74E-12
vg0216616004 sf0216610134 2 16616004 1.01E-12 1.67E-06
vg0217412542 sf0217406672 2 17412542 1.02E-12 2.42E-06
vg1210415243 sf1210412656 12 10415243 1.26E-12 2.76E-06
vg0217677605 sf0217671735 2 17677605 2.10E-12 2.76E-06
vg1114473442 sf1114009759 11 14473442 8.17E-12 1.54E-06
vg0217612660 sf0217606790 2 17612660 3.70E-10 5.64E-08
vg0216721532 sf0216715662 2 16721532 1.06E-09 1.23E-07
vg1112889066 sf1112425387 11 12889066 2.02E-09 2.57E-07
vg0216876069 sf0216870199 2 16876069 2.12E-09 4.96E-09
vg0216661985 sf0216656115 2 16661985 2.92E-09 1.01E-06
vg0230571236 sf0230565367 2 30571236 9.03E-07 3.51E-06
vg1211683413 sf1211680749 12 11683413 NA 3.60E-06