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 mr1100 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
vg0406266784 sf0406262224 4 6266784 5.48E-151 1.09E-33
vg0406526555 sf0406521998 4 6526555 1.10E-150 1.79E-34
vg0411344776 sf0411335479 4 11344776 3.58E-117 NA
vg0307375905 sf0307374903 3 7375905 1.11E-111 NA
vg0232341467 sf0232335598 2 32341467 1.27E-109 NA
vg0914461514 sf0914460513 9 14461514 3.64E-109 NA
vg0914065568 sf0914064567 9 14065568 6.46E-106 4.50E-07
vg0817328107 sf0817325393 8 17328107 6.81E-104 6.12E-10
vg0406521772 sf0406517215 4 6521772 NA 3.45E-15
vg0222745337 sf0222739468 2 22745337 NA 6.26E-12
vg0222719698 sf0222713829 2 22719698 NA 2.63E-11
vg0406532594 sf0406528037 4 6532594 NA 6.37E-10
vg1209905874 sf1209903284 12 9905874 NA 1.51E-09
vg0406289584 sf0406285024 4 6289584 NA 3.83E-09
vg0407565723 sf0407560992 4 7565723 NA 5.65E-09
vg0406449684 sf0406445127 4 6449684 NA 2.56E-08
vg0431078210 sf0430893099 4 31078210 NA 4.61E-08
vg1004522984 sf1004539522 10 4522984 NA 6.94E-08
vg0204901081 sf0204901078 2 4901081 NA 1.12E-07
vg0431076967 sf0430891856 4 31076967 NA 1.28E-07
vg0411635497 sf0411626203 4 11635497 NA 1.87E-07
vg0124952235 sf0124951191 1 24952235 NA 3.39E-07
vg0135049651 sf0135048608 1 35049651 NA 3.65E-07
vg1221081688 sf1221048238 12 21081688 NA 5.72E-07
vg0412173881 sf0412164592 4 12173881 NA 6.09E-07
vg0223096991 sf0223091122 2 23096991 NA 6.09E-07
vg0313207043 sf0313205761 3 13207043 NA 1.07E-06
vg1216352950 sf1216350246 12 16352950 NA 2.50E-06
vg0313656312 sf0313655029 3 13656312 NA 3.00E-06