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 mr1496 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 2.84E-14 5.79E-10
vg0336193973 sf0336186899 3 36193973 2.48E-13 1.22E-08
vg0224173859 sf0224167990 2 24173859 3.15E-13 1.41E-10
vg0136191693 sf0136190650 1 36191693 4.12E-13 1.31E-10
vg0915284648 sf0915283647 9 15284648 6.10E-13 6.57E-07
vg0308535729 sf0308534667 3 8535729 1.14E-12 8.01E-08
vg1016339056 sf1016267832 10 16339056 4.02E-12 6.51E-08
vg0141320383 sf0141319340 1 41320383 6.86E-12 6.96E-08
vg0515214258 sf0515156800 5 15214258 1.25E-11 1.01E-07
vg1201867679 sf1201866676 12 1867679 1.41E-11 9.41E-08
vg0727970899 sf0727969906 7 27970899 1.48E-11 8.38E-08
vg0625443240 sf0625442243 6 25443240 2.20E-11 4.36E-08
vg0504952991 sf0504952969 5 4952991 3.51E-11 6.68E-08
vg1001348300 sf1001347277 10 1348300 9.84E-11 1.76E-07
vg0424049928 sf0423864789 4 24049928 1.09E-10 5.53E-07
vg0432345183 sf0432160072 4 32345183 3.43E-10 1.11E-09
vg1117137503 sf1116671355 11 17137503 2.21E-09 1.55E-08
vg0432825867 sf0432640753 4 32825867 2.59E-08 1.07E-07
vg0133772255 sf0133771211 1 33772255 9.34E-08 8.22E-08
vg0708623561 sf0708622566 7 8623561 1.02E-07 NA
vg0600020896 sf0600019896 6 20896 1.23E-07 3.76E-08
vg0233656481 sf0233650612 2 33656481 4.81E-07 NA
vg0102022843 sf0102021843 1 2022843 1.00E-06 NA
vg0714435734 sf0714434741 7 14435734 2.24E-06 1.84E-07
vg0621728622 sf0621727625 6 21728622 2.43E-06 1.75E-07