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 mr1219 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
vg0605262883 sf0605261884 6 5262883 4.44E-41 2.17E-21
vg0605311849 sf0605310850 6 5311849 1.77E-38 1.02E-22
vg0605162589 sf0605161590 6 5162589 1.85E-14 1.58E-07
vg0918154446 sf0918153445 9 18154446 5.30E-14 NA
vg1204986534 sf1204985520 12 4986534 6.00E-14 1.76E-06
vg0605412605 sf0605411606 6 5412605 1.71E-13 3.16E-06
vg0605126671 sf0605125672 6 5126671 2.19E-13 4.63E-07
vg0918159853 sf0918158852 9 18159853 2.55E-13 1.13E-07
vg0328327940 sf0328320994 3 28327940 4.02E-13 NA
vg0500532312 sf0500532312 5 532312 5.16E-13 2.06E-06
vg0209219211 sf0209219209 2 9219211 3.16E-12 1.67E-07
vg0920819355 sf0920818874 9 20819355 5.04E-10 1.36E-06
vg0434382078 sf0434196972 4 34382078 4.96E-08 1.05E-07
vg0519823381 sf0519760857 5 19823381 5.06E-08 NA
vg1124667824 sf1124201664 11 24667824 2.64E-07 1.03E-06
vg1202093389 sf1202092387 12 2093389 NA 3.90E-07
vg0612526873 sf0612525874 6 12526873 NA 1.38E-06
vg0900257645 sf0900256645 9 257645 NA 1.48E-06
vg0327760034 sf0327753087 3 27760034 NA 4.12E-06
vg0137580287 sf0137579244 1 37580287 NA 4.17E-06