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 mr1055 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 1.79E-104 1.91E-54
vg1209571445 sf1209568854 12 9571445 1.11E-67 1.53E-28
vg1223872806 sf1223839259 12 23872806 2.13E-47 6.13E-10
vg1223827289 sf1223793742 12 23827289 5.28E-42 1.21E-10
vg0410423427 sf0410414126 4 10423427 1.63E-31 6.81E-10
vg1212726422 sf1212723761 12 12726422 1.83E-30 5.83E-10
vg1017708903 sf1017637676 10 17708903 1.59E-23 5.45E-08
vg1219898289 sf1219869759 12 19898289 2.40E-21 7.52E-07
vg1215471234 sf1215468531 12 15471234 4.35E-18 1.05E-09
vg0631078445 sf0631077447 6 31078445 1.55E-16 7.57E-11
vg1214850093 sf1214847434 12 14850093 1.50E-15 7.81E-12
vg1215789548 sf1215786845 12 15789548 1.37E-13 2.50E-07
vg1216282973 sf1216280269 12 16282973 1.60E-12 3.56E-07
vg1216279961 sf1216277257 12 16279961 NA 1.40E-14
vg1207811491 sf1207808897 12 7811491 NA 4.83E-11
vg1215976836 sf1215974132 12 15976836 NA 1.77E-09
vg1223678969 sf1223645422 12 23678969 NA 1.65E-08
vg1208959876 sf1208957284 12 8959876 NA 2.66E-07
vg0416574457 sf0416402498 4 16574457 NA 2.80E-07
vg0707344915 sf0707343920 7 7344915 NA 3.81E-07
vg1215304178 sf1215301476 12 15304178 NA 9.26E-07