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 mr1079 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
vg1215977007 sf1215974303 12 15977007 4.35E-86 1.85E-39
vg1209571445 sf1209568854 12 9571445 4.00E-58 6.17E-22
vg1210693559 sf1210690972 12 10693559 1.07E-54 4.99E-24
vg1223872806 sf1223839259 12 23872806 1.49E-44 2.87E-09
vg1223827289 sf1223793742 12 23827289 1.11E-40 2.17E-09
vg1212726422 sf1212723761 12 12726422 1.29E-30 1.47E-09
vg1213439429 sf1213436767 12 13439429 1.45E-27 1.36E-07
vg0410423427 sf0410414126 4 10423427 5.13E-24 4.00E-06
vg1214872776 sf1214870117 12 14872776 1.15E-17 6.58E-08
vg1215420354 sf1215417652 12 15420354 1.36E-17 2.17E-09
vg1217556649 sf1217550604 12 17556649 2.34E-14 5.26E-07
vg1214839103 sf1214836444 12 14839103 2.42E-14 5.61E-10
vg1214706284 sf1214703625 12 14706284 3.79E-14 3.37E-09
vg1216279961 sf1216277257 12 16279961 NA 2.41E-13
vg1215976836 sf1215974132 12 15976836 NA 3.82E-09
vg1207811491 sf1207808897 12 7811491 NA 9.42E-09
vg1217327067 sf1217321022 12 17327067 NA 1.12E-08
vg1223678969 sf1223645422 12 23678969 NA 2.68E-08
vg1216524318 sf1216521611 12 16524318 NA 1.51E-07
vg0400455007 sf0400454005 4 455007 NA 2.21E-07
vg1215305027 sf1215302325 12 15305027 NA 2.28E-07
vg0416574457 sf0416402498 4 16574457 NA 3.61E-07
vg1214513714 sf1214511055 12 14513714 NA 3.78E-07
vg0224207855 sf0224201986 2 24207855 NA 6.74E-07