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 mr1765 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
vg0335000939 sf0334993809 3 35000939 1.43E-12 1.08E-08
vg0523114802 sf0523052243 5 23114802 2.12E-12 2.22E-06
vg1003025097 sf1003024074 10 3025097 7.54E-12 NA
vg0619827978 sf0619826981 6 19827978 2.08E-11 NA
vg0226766538 sf0226760669 2 26766538 3.22E-11 NA
vg0202722002 sf0202722000 2 2722002 1.06E-10 8.69E-07
vg0711698103 sf0711697109 7 11698103 2.27E-10 NA
vg0615347149 sf0615346150 6 15347149 2.82E-10 8.54E-07
vg1221736592 sf1221703139 12 21736592 2.85E-10 2.78E-06
vg1010713156 sf1010641977 10 10713156 4.89E-10 2.24E-07
vg0400108977 sf0400107977 4 108977 1.22E-09 1.89E-06
vg0327416803 sf0327409856 3 27416803 4.83E-09 1.37E-06
vg1011002863 sf1010931683 10 11002863 2.26E-08 4.56E-07
vg0819968714 sf0819966001 8 19968714 2.57E-08 3.19E-06
vg1011003755 sf1010932575 10 11003755 NA 2.11E-08
vg0722277838 sf0722276845 7 22277838 NA 1.10E-07
vg0400357479 sf0400356479 4 357479 NA 2.11E-07
vg0627990543 sf0627989545 6 27990543 NA 9.86E-07
vg1005384319 sf1005400856 10 5384319 NA 1.42E-06
vg0628022404 sf0628021406 6 28022404 NA 1.62E-06
vg0400468558 sf0400467556 4 468558 NA 1.67E-06
vg0605613230 sf0605612231 6 5613230 NA 2.92E-06
vg0334732696 sf0334725566 3 34732696 NA 3.16E-06
vg1004535011 sf1004551549 10 4535011 NA 3.42E-06
vg0334733128 sf0334725998 3 34733128 NA 3.78E-06