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 mr1080 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
vg0406526555 sf0406521998 4 6526555 5.18E-161 4.12E-36
vg0411344776 sf0411335479 4 11344776 7.21E-125 NA
vg0406579445 sf0406574888 4 6579445 1.95E-121 6.02E-12
vg0122833397 sf0122832353 1 22833397 7.01E-118 NA
vg1016650869 sf1016579642 10 16650869 1.53E-117 NA
vg0307375905 sf0307374903 3 7375905 1.79E-117 NA
vg0912928457 sf0912927456 9 12928457 5.80E-114 8.59E-09
vg0406575363 sf0406570806 4 6575363 1.35E-111 5.55E-07
vg0412479470 sf0412470185 4 12479470 2.27E-106 5.60E-08
vg0406521772 sf0406517215 4 6521772 NA 1.88E-14
vg0407565723 sf0407560992 4 7565723 NA 6.77E-12
vg0411637990 sf0411628696 4 11637990 NA 1.76E-11
vg0406362113 sf0406357553 4 6362113 NA 2.47E-10
vg0406532594 sf0406528037 4 6532594 NA 3.06E-09
vg0817329442 sf0817326728 8 17329442 NA 2.29E-08
vg0125080782 sf0125079738 1 25080782 NA 3.21E-08
vg0306151794 sf0306150794 3 6151794 NA 6.10E-08
vg0406449684 sf0406445127 4 6449684 NA 7.09E-08
vg1216535929 sf1216533222 12 16535929 NA 1.04E-07
vg1216524512 sf1216521805 12 16524512 NA 1.23E-07
vg1209897018 sf1209894428 12 9897018 NA 1.51E-07
vg0313207043 sf0313205761 3 13207043 NA 2.16E-07
vg1016503494 sf1016432267 10 16503494 NA 3.61E-07
vg0900608673 sf0900607673 9 608673 NA 7.00E-07
vg0406537255 sf0406532698 4 6537255 NA 7.08E-07
vg0806423507 sf0806422512 8 6423507 NA 7.18E-07
vg1109141672 sf1109136251 11 9141672 NA 9.09E-07
vg0222719698 sf0222713829 2 22719698 NA 9.80E-06