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 mr1841 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
vg1125118463 sf1124652303 11 25118463 2.75E-63 9.10E-46
vg1124959930 sf1124493770 11 24959930 1.38E-39 6.15E-13
vg0105168999 sf0105167999 1 5168999 8.64E-38 7.15E-08
vg0715799020 sf0715798027 7 15799020 1.91E-37 3.55E-06
vg0715763923 sf0715762930 7 15763923 2.89E-37 1.04E-06
vg0706531615 sf0706530620 7 6531615 3.97E-37 NA
vg1124875808 sf1124409648 11 24875808 1.88E-35 1.05E-19
vg1124989458 sf1124523298 11 24989458 6.26E-32 1.05E-29
vg1124968994 sf1124502834 11 24968994 NA 4.87E-27
vg1124986792 sf1124520632 11 24986792 NA 4.43E-26
vg1125112695 sf1124646535 11 25112695 NA 7.48E-17
vg1125080303 sf1124614143 11 25080303 NA 2.78E-15
vg1125089512 sf1124623352 11 25089512 NA 4.44E-15
vg1125393477 sf1124927316 11 25393477 NA 7.73E-15
vg1125233443 sf1124767283 11 25233443 NA 1.52E-14
vg1125110574 sf1124644414 11 25110574 NA 5.77E-13
vg1125079769 sf1124613609 11 25079769 NA 1.23E-11
vg0328637867 sf0328630920 3 28637867 NA 1.45E-11
vg1125389716 sf1124923555 11 25389716 NA 1.68E-11
vg1124857333 sf1124391173 11 24857333 NA 1.62E-10
vg1125257504 sf1124791344 11 25257504 NA 1.86E-09
vg1124929928 sf1124463768 11 24929928 NA 3.28E-09
vg0307571121 sf0307570059 3 7571121 NA 3.98E-09
vg1128793169 sf1128269948 11 28793169 NA 7.57E-09
vg1122505213 sf1122039084 11 22505213 NA 8.87E-09
vg0621172424 sf0621171427 6 21172424 NA 1.17E-08
vg1128437977 sf1127914756 11 28437977 NA 1.19E-08
vg1008205727 sf1008134589 10 8205727 NA 1.23E-08
vg1120705127 sf1120239030 11 20705127 NA 6.29E-07
vg0503762591 sf0503762568 5 3762591 NA 1.96E-06