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 mr1018 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
vg1215968758 sf1215966054 12 15968758 2.53E-14 1.19E-11
vg1210709343 sf1210706756 12 10709343 5.61E-13 1.65E-10
vg1223872806 sf1223839259 12 23872806 1.40E-09 2.16E-06
vg1017701671 sf1017630444 10 17701671 2.28E-08 NA
vg1207825747 sf1207823153 12 7825747 2.31E-08 1.63E-08
vg0402676745 sf0402672349 4 2676745 6.93E-08 1.97E-08
vg0217612660 sf0217606790 2 17612660 1.26E-07 4.41E-06
vg0220337774 sf0220331906 2 20337774 1.56E-07 2.08E-06
vg1206837224 sf1206836114 12 6837224 2.17E-07 1.35E-06
vg0715978134 sf0715977141 7 15978134 2.71E-07 6.64E-08
vg1220250941 sf1220222383 12 20250941 2.86E-07 6.61E-07
vg1121955520 sf1121489391 11 21955520 3.61E-07 1.56E-06
vg1216192507 sf1216189803 12 16192507 5.13E-07 1.26E-06
vg1209050414 sf1209047823 12 9050414 1.45E-06 4.72E-07
vg0706671410 sf0706670415 7 6671410 2.02E-06 4.61E-06
vg1215096337 sf1215093674 12 15096337 2.47E-06 4.56E-06
vg0324116659 sf0324114738 3 24116659 2.75E-06 1.76E-06
vg0223196089 sf0223190220 2 23196089 8.58E-06 3.79E-06