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 mr1301 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
vg1210300519 sf1210297932 12 10300519 4.53E-23 5.20E-11
vg1209292727 sf1209290137 12 9292727 2.26E-22 3.08E-11
vg1217578105 sf1217572060 12 17578105 6.51E-19 NA
vg1223873419 sf1223839872 12 23873419 1.14E-16 NA
vg0408294814 sf0408290088 4 8294814 2.08E-16 4.44E-07
vg1215854982 sf1215852278 12 15854982 4.62E-16 1.50E-06
vg0215909137 sf0215903267 2 15909137 1.37E-15 NA
vg0504497819 sf0504497796 5 4497819 5.18E-15 1.84E-06
vg0315778980 sf0315777627 3 15778980 1.40E-13 2.09E-06
vg0613607454 sf0613606455 6 13607454 1.43E-13 5.68E-07
vg0305260839 sf0305259839 3 5260839 2.25E-12 8.01E-07
vg0704234686 sf0704233687 7 4234686 7.23E-12 8.48E-07
vg0608080641 sf0608079642 6 8080641 4.05E-11 NA
vg0605146424 sf0605145425 6 5146424 4.90E-10 8.69E-06
vg1205317195 sf1205316181 12 5317195 3.18E-09 2.11E-07
vg0718523777 sf0718522784 7 18523777 3.62E-09 2.25E-07
vg0721134698 sf0721133705 7 21134698 6.63E-09 1.27E-08
vg1214865164 sf1214862505 12 14865164 3.51E-08 NA
vg0720881549 sf0720880556 7 20881549 6.72E-08 3.42E-07
vg1205368460 sf1205367446 12 5368460 NA 1.04E-06
vg0431583357 sf0431398253 4 31583357 NA 2.18E-06
vg0810856819 sf0810855824 8 10856819 NA 3.41E-06
vg0721486566 sf0721485573 7 21486566 NA 3.52E-06
vg0722579980 sf0722578987 7 22579980 NA 3.94E-06
vg0729288258 sf0729287266 7 29288258 NA 4.33E-06
vg0800649368 sf0800648368 8 649368 NA 4.91E-06