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 mr1542 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
vg0314567323 sf0314566010 3 14567323 2.75E-106 1.95E-62
vg0314571719 sf0314570406 3 14571719 7.34E-105 1.25E-62
vg0314521197 sf0314519885 3 14521197 2.37E-19 2.90E-14
vg0314512032 sf0314510720 3 14512032 8.58E-19 1.16E-16
vg0314719214 sf0314717901 3 14719214 3.34E-18 3.46E-09
vg0314683577 sf0314682264 3 14683577 3.77E-17 4.80E-08
vg0314644172 sf0314642859 3 14644172 1.70E-15 2.53E-06
vg0314639120 sf0314637807 3 14639120 2.15E-15 5.68E-08
vg0314575945 sf0314574632 3 14575945 2.18E-15 4.72E-09
vg0314860588 sf0314859235 3 14860588 8.74E-15 1.25E-09
vg0314638773 sf0314637460 3 14638773 8.23E-14 1.89E-06
vg0312726265 sf0312724983 3 12726265 1.05E-12 2.75E-06
vg0314579234 sf0314577921 3 14579234 1.15E-11 3.61E-09
vg1016561576 sf1016490349 10 16561576 2.19E-09 5.49E-07
vg0314726805 sf0314725492 3 14726805 1.23E-07 4.12E-06
vg1218395203 sf1218366639 12 18395203 1.71E-07 NA
vg0314553734 sf0314552422 3 14553734 NA 3.98E-10
vg0615685726 sf0615684728 6 15685726 NA 1.09E-06
vg0329978728 sf0329971767 3 29978728 NA 2.95E-06
vg0617084846 sf0617083849 6 17084846 NA 3.60E-06