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 mr1936 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
vg0421387824 sf0421215877 4 21387824 2.53E-14 6.83E-11
vg0421388196 sf0421216249 4 21388196 8.41E-13 3.88E-09
vg1219134304 sf1219105740 12 19134304 7.94E-11 2.24E-08
vg0504687974 sf0504687951 5 4687974 1.90E-09 6.68E-06
vg0336193973 sf0336186899 3 36193973 1.97E-09 1.90E-07
vg1203255841 sf1203254844 12 3255841 2.38E-09 NA
vg1204507349 sf1204506337 12 4507349 5.33E-09 6.93E-07
vg1126461419 sf1125989832 11 26461419 6.13E-09 1.50E-06
vg0728000317 sf0727999324 7 28000317 6.37E-09 1.53E-06
vg0334827866 sf0334820736 3 34827866 1.03E-08 6.10E-07
vg1002009944 sf1002008921 10 2009944 3.35E-08 1.99E-06
vg0628759426 sf0628758428 6 28759426 4.16E-08 4.73E-06
vg1117137503 sf1116671355 11 17137503 4.44E-08 5.08E-08
vg0504952991 sf0504952969 5 4952991 1.58E-07 1.40E-06
vg1014514985 sf1014443751 10 14514985 2.07E-07 2.96E-06
vg1004727190 sf1004743727 10 4727190 2.45E-07 2.87E-06
vg0819366916 sf0819364203 8 19366916 3.56E-07 3.41E-06
vg0714480545 sf0714479552 7 14480545 1.05E-06 1.59E-06
vg0819421680 sf0819418967 8 19421680 1.13E-06 2.64E-07
vg0812050496 sf0812049501 8 12050496 7.94E-06 NA
vg1004081523 sf1004080499 10 4081523 8.75E-06 NA
vg0612574686 sf0612573687 6 12574686 NA 1.92E-06
vg0307075857 sf0307074855 3 7075857 NA 2.36E-06
vg1204324436 sf1204323424 12 4324436 NA 2.39E-06