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 mr1013 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
vg0433918375 sf0433733272 4 33918375 3.14E-25 4.09E-15
vg1208201103 sf1208198509 12 8201103 2.07E-23 6.43E-07
vg0235315290 sf0235309421 2 35315290 1.04E-21 4.72E-07
vg0529082765 sf0529020120 5 29082765 2.69E-21 2.02E-06
vg0304269557 sf0304268559 3 4269557 5.91E-21 5.75E-06
vg0113480569 sf0113479543 1 13480569 1.47E-20 5.78E-08
vg0136958261 sf0136957218 1 36958261 1.93E-19 4.20E-08
vg1124276697 sf1123810567 11 24276697 8.00E-19 2.21E-06
vg0226007492 sf0226001623 2 26007492 2.63E-18 3.28E-06
vg0120090794 sf0120089749 1 20090794 7.01E-18 2.38E-06
vg0130113615 sf0130112570 1 30113615 2.65E-17 9.63E-06
vg0412235189 sf0412225900 4 12235189 1.36E-16 6.63E-07
vg0432518407 sf0432333299 4 32518407 2.22E-16 6.85E-08
vg0826395442 sf0826392728 8 26395442 1.20E-15 4.23E-06
vg0224787316 sf0224781447 2 24787316 NA 1.23E-07
vg0433948721 sf0433763617 4 33948721 NA 5.38E-07
vg0224416114 sf0224410245 2 24416114 NA 7.20E-07
vg0136843188 sf0136842145 1 36843188 NA 9.96E-07
vg0200487383 sf0200487383 2 487383 NA 1.16E-06
vg0405425386 sf0405420827 4 5425386 NA 1.58E-06
vg1017934811 sf1017863583 10 17934811 NA 1.82E-06
vg0432638617 sf0432453506 4 32638617 NA 2.32E-06
vg0805244886 sf0805243889 8 5244886 NA 2.57E-06
vg0915457997 sf0915456996 9 15457997 NA 7.27E-06