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 mr1914 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
vg0217023878 sf0217018008 2 17023878 1.24E-60 1.61E-31
vg0217071746 sf0217065876 2 17071746 1.71E-59 3.09E-34
vg1108225523 sf1108220133 11 8225523 2.07E-23 NA
vg1128516527 sf1127993306 11 28516527 7.20E-23 8.74E-08
vg1220336317 sf1220307759 12 20336317 8.04E-21 5.13E-07
vg0218856450 sf0218850581 2 18856450 3.41E-19 3.01E-06
vg1015182556 sf1015111324 10 15182556 9.72E-19 NA
vg1216728961 sf1216722915 12 16728961 7.76E-18 1.29E-06
vg0212875961 sf0212875957 2 12875961 1.25E-16 2.22E-07
vg0217555934 sf0217550064 2 17555934 2.04E-15 6.94E-07
vg0212130167 sf0212130163 2 12130167 5.62E-15 4.22E-08
vg0216424953 sf0216419083 2 16424953 1.68E-14 1.07E-07
vg0217186740 sf0217180870 2 17186740 2.07E-13 2.17E-06
vg0213900866 sf0213894996 2 13900866 8.59E-13 3.18E-08
vg0215426540 sf0215420670 2 15426540 3.20E-12 1.06E-06
vg1216723603 sf1216717557 12 16723603 5.05E-10 4.06E-07
vg0217461610 sf0217455740 2 17461610 4.81E-09 2.73E-06
vg0219768664 sf0219762796 2 19768664 1.85E-08 4.35E-06
vg0216627913 sf0216622043 2 16627913 2.20E-08 1.52E-09
vg0917229602 sf0917228601 9 17229602 NA 4.80E-06