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 mr1945 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 6.73E-55 1.28E-39
vg1124935001 sf1124468841 11 24935001 5.99E-24 2.44E-21
vg0608084642 sf0608083643 6 8084642 2.72E-23 4.71E-07
vg0105153133 sf0105152133 1 5153133 3.52E-23 1.32E-06
vg0706798160 sf0706797165 7 6798160 1.36E-22 NA
vg0608086564 sf0608085565 6 8086564 3.42E-22 1.46E-09
vg0706531615 sf0706530620 7 6531615 5.91E-22 NA
vg1124875808 sf1124409648 11 24875808 1.55E-21 5.74E-13
vg1124322062 sf1123855932 11 24322062 1.00E-20 2.71E-08
vg1124989458 sf1124523298 11 24989458 1.06E-20 2.86E-18
vg0124723474 sf0124722430 1 24723474 4.63E-20 1.59E-08
vg0307590023 sf0307588961 3 7590023 1.92E-18 2.64E-09
vg1125089512 sf1124623352 11 25089512 NA 1.10E-11
vg1125080303 sf1124614143 11 25080303 NA 1.81E-11
vg1125105649 sf1124639489 11 25105649 NA 2.13E-11
vg0328637867 sf0328630920 3 28637867 NA 3.09E-11
vg1124453926 sf1123987766 11 24453926 NA 4.97E-11
vg1124988847 sf1124522687 11 24988847 NA 1.12E-10
vg1125393477 sf1124927316 11 25393477 NA 1.40E-10
vg1125229010 sf1124762850 11 25229010 NA 6.34E-10
vg1124929928 sf1124463768 11 24929928 NA 3.44E-09
vg0901346489 sf0901345489 9 1346489 NA 3.91E-09
vg1125079769 sf1124613609 11 25079769 NA 7.55E-09
vg0528175919 sf0528113274 5 28175919 NA 1.11E-08
vg1124807320 sf1124341160 11 24807320 NA 2.21E-08
vg1214637266 sf1214634606 12 14637266 NA 9.31E-07