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 mr1240 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 3.79E-21 9.12E-16
vg0336193973 sf0336186899 3 36193973 3.37E-18 3.65E-13
vg0421388196 sf0421216249 4 21388196 1.17E-17 9.60E-12
vg0727970899 sf0727969906 7 27970899 8.51E-15 1.38E-08
vg0504687974 sf0504687951 5 4687974 1.90E-14 1.53E-08
vg1203255841 sf1203254844 12 3255841 2.89E-14 3.17E-07
vg0308535729 sf0308534667 3 8535729 4.26E-14 2.58E-08
vg1016339056 sf1016267832 10 16339056 6.57E-14 3.18E-09
vg1001348300 sf1001347277 10 1348300 7.04E-13 1.13E-07
vg1126461419 sf1125989832 11 26461419 9.39E-13 1.69E-08
vg1004727190 sf1004743727 10 4727190 4.00E-12 5.49E-09
vg0504952991 sf0504952969 5 4952991 5.74E-12 1.02E-08
vg1201867679 sf1201866676 12 1867679 1.66E-11 9.25E-08
vg1117137503 sf1116671355 11 17137503 3.45E-11 1.25E-09
vg1002009944 sf1002008921 10 2009944 5.96E-11 3.26E-08
vg0628759426 sf0628758428 6 28759426 6.68E-11 2.48E-08
vg0906313471 sf0906312471 9 6313471 6.85E-11 1.06E-07
vg0819366916 sf0819364203 8 19366916 2.26E-10 3.89E-08
vg0224540597 sf0224534728 2 24540597 8.47E-10 1.17E-07
vg1205542061 sf1205541047 12 5542061 4.50E-09 2.00E-07
vg0819421680 sf0819418967 8 19421680 1.11E-08 3.48E-08
vg0714480545 sf0714479552 7 14480545 2.09E-07 1.51E-07
vg1208630676 sf1208628083 12 8630676 NA 3.57E-08