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 mr1075 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
vg0222742146 sf0222736277 2 22742146 1.71E-61 1.64E-39
vg0222739831 sf0222733962 2 22739831 5.74E-61 1.46E-40
vg0223663745 sf0223657876 2 23663745 1.22E-16 1.02E-11
vg0224640486 sf0224634617 2 24640486 4.73E-14 1.03E-06
vg0120457652 sf0120456607 1 20457652 8.51E-14 NA
vg0224832365 sf0224826496 2 24832365 2.27E-13 3.38E-07
vg0226061785 sf0226055916 2 26061785 3.43E-13 8.03E-07
vg0224639472 sf0224633603 2 24639472 6.16E-13 7.08E-07
vg0224382271 sf0224376402 2 24382271 8.38E-13 3.79E-09
vg1112606104 sf1112142307 11 12606104 8.84E-13 1.91E-06
vg0222765370 sf0222759501 2 22765370 8.50E-12 7.15E-07
vg0226003155 sf0225997286 2 26003155 3.40E-11 2.55E-07
vg0223973381 sf0223967512 2 23973381 3.93E-11 1.84E-06
vg0224508619 sf0224502750 2 24508619 6.70E-11 1.09E-06
vg0222672664 sf0222666795 2 22672664 7.47E-11 1.17E-11
vg0223506504 sf0223500635 2 23506504 8.95E-11 1.16E-06
vg0224872829 sf0224866960 2 24872829 9.43E-10 4.98E-06
vg0120126603 sf0120125558 1 20126603 2.46E-09 NA
vg0222799001 sf0222793132 2 22799001 1.54E-08 1.34E-06
vg0223048890 sf0223043021 2 23048890 1.04E-07 3.96E-07
vg0610678495 sf0610677496 6 10678495 2.87E-07 2.79E-06
vg0401805850 sf0401801445 4 1805850 NA 2.08E-06
vg0223043250 sf0223037381 2 23043250 NA 2.68E-06
vg0225413648 sf0225407779 2 25413648 NA 3.04E-06