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 mr1784 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
vg1018891503 sf1018820059 10 18891503 2.29E-17 4.85E-07
vg1019101727 sf1019030284 10 19101727 2.07E-16 1.96E-07
vg1219345800 sf1219317270 12 19345800 4.58E-14 NA
vg0434375534 sf0434190428 4 34375534 7.37E-14 NA
vg1200274541 sf1200273541 12 274541 9.24E-13 2.29E-06
vg0131887637 sf0131886593 1 31887637 9.79E-13 NA
vg0700837076 sf0700836076 7 837076 1.98E-12 3.31E-07
vg0318954218 sf0318952978 3 18954218 3.21E-12 3.35E-06
vg0318195210 sf0318193992 3 18195210 5.48E-12 4.18E-07
vg0402280802 sf0402276397 4 2280802 8.07E-11 1.67E-06
vg0133312519 sf0133311475 1 33312519 2.04E-10 NA
vg0432569391 sf0432384282 4 32569391 NA 6.75E-07