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 mr1123 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 5.56E-17 6.15E-12
vg0108582948 sf0108581948 1 8582948 1.65E-14 5.88E-10
vg0504875404 sf0504875381 5 4875404 4.68E-13 4.98E-08
vg0700863821 sf0700862821 7 863821 8.53E-12 2.94E-08
vg0424049928 sf0423864789 4 24049928 1.85E-11 1.57E-07
vg0103158009 sf0103157009 1 3158009 2.09E-11 4.02E-07
vg0336193973 sf0336186899 3 36193973 2.85E-11 1.44E-07
vg0136191693 sf0136190650 1 36191693 1.43E-10 6.85E-08
vg0142062769 sf0142061726 1 42062769 1.46E-10 3.73E-08
vg0628759426 sf0628758428 6 28759426 1.74E-10 2.17E-07
vg0708623561 sf0708622566 7 8623561 1.96E-10 4.56E-07
vg1201867679 sf1201866676 12 1867679 2.82E-10 2.65E-07
vg0709675216 sf0709674222 7 9675216 4.62E-10 4.16E-09
vg1126461419 sf1125989832 11 26461419 7.04E-10 1.28E-07
vg1205542061 sf1205541047 12 5542061 9.23E-10 1.15E-07
vg1004727190 sf1004743727 10 4727190 1.50E-09 4.20E-07
vg0224215161 sf0224209292 2 24215161 5.91E-09 7.43E-09
vg0432345183 sf0432160072 4 32345183 1.41E-07 1.89E-07
vg0622630104 sf0622629107 6 22630104 2.16E-07 8.17E-06
vg0220994638 sf0220988770 2 20994638 1.14E-06 2.01E-07
vg1110012449 sf1110007026 11 10012449 3.42E-06 1.76E-06
vg1223974671 sf1223941124 12 23974671 3.52E-06 NA
vg0804875587 sf0804874590 8 4875587 NA 2.44E-07