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 mr1848 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
vg0626920669 sf0626919672 6 26920669 3.34E-09 3.34E-09
vg0228241702 sf0228235833 2 28241702 1.20E-08 1.20E-08
vg0915839206 sf0915838205 9 15839206 9.76E-08 9.77E-08
vg0125387519 sf0125386475 1 25387519 1.53E-07 1.54E-07
vg0231332457 sf0231326588 2 31332457 8.16E-07 8.18E-07
vg1127979405 sf1127507791 11 27979405 8.34E-07 8.34E-07
vg1204328784 sf1204327772 12 4328784 9.91E-07 9.92E-07
vg0306112685 sf0306111685 3 6112685 1.31E-06 1.31E-06
vg0701185368 sf0701184368 7 1185368 1.32E-06 1.32E-06
vg1225529316 sf1225495711 12 25529316 1.38E-06 1.38E-06
vg0114207760 sf0114206734 1 14207760 1.49E-06 1.49E-06
vg0427530535 sf0427345396 4 27530535 1.69E-06 1.69E-06
vg0234351024 sf0234345155 2 34351024 2.38E-06 2.38E-06
vg1224668311 sf1224634765 12 24668311 2.40E-06 2.41E-06
vg0913641299 sf0913640298 9 13641299 2.51E-06 2.51E-06
vg0429234433 sf0429049290 4 29234433 2.56E-06 2.57E-06
vg0806613735 sf0806612740 8 6613735 2.77E-06 2.78E-06
vg0210199468 sf0210199466 2 10199468 3.26E-06 3.26E-06
vg1103560667 sf1103556570 11 3560667 3.61E-06 3.61E-06
vg0729298014 sf0729297022 7 29298014 4.03E-06 4.03E-06