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 mr1693 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
vg0212235071 sf0212235067 2 12235071 2.43E-11 2.28E-07
vg0721330014 sf0721329021 7 21330014 1.24E-10 6.73E-07
vg1123449893 sf1122983763 11 23449893 1.57E-10 4.68E-06
vg1011369792 sf1011298611 10 11369792 1.79E-10 2.95E-06
vg0810920351 sf0810919356 8 10920351 2.33E-10 7.29E-06
vg0402373617 sf0402369212 4 2373617 2.89E-10 2.96E-07
vg0811700880 sf0811699885 8 11700880 3.38E-10 1.93E-06
vg0722260306 sf0722259313 7 22260306 1.07E-09 2.05E-06
vg1107088655 sf1107084400 11 7088655 1.46E-08 8.96E-07
vg1124199328 sf1123733198 11 24199328 6.26E-08 5.14E-07
vg0141835925 sf0141834882 1 41835925 3.27E-07 3.54E-06
vg1127362220 sf1126890607 11 27362220 5.31E-07 3.70E-06
vg0316570538 sf0316569183 3 16570538 2.21E-06 NA
vg0303447913 sf0303446909 3 3447913 2.84E-06 3.43E-06
vg1005803839 sf1005820377 10 5803839 4.07E-06 NA
vg0131108800 sf0131107756 1 31108800 NA 1.14E-06
vg0721638290 sf0721637297 7 21638290 NA 1.44E-06
vg0825980691 sf0825977977 8 25980691 NA 3.89E-06
vg0419990751 sf0419818787 4 19990751 NA 4.28E-06
vg1021136565 sf1021065044 10 21136565 NA 4.69E-06