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 mr1609 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
vg1125118463 sf1124652303 11 25118463 1.26E-16 1.26E-16
vg1124875808 sf1124409648 11 24875808 4.91E-13 4.91E-13
vg1124857333 sf1124391173 11 24857333 1.17E-09 1.17E-09
vg0901835907 sf0901834907 9 1835907 1.43E-07 1.43E-07
vg0606540226 sf0606539227 6 6540226 3.71E-07 3.71E-07
vg1128817624 sf1128294403 11 28817624 4.85E-07 4.85E-07
vg1125022392 sf1124556232 11 25022392 4.90E-07 4.90E-07
vg0622512118 sf0622511121 6 22512118 5.67E-07 5.67E-07
vg0821045762 sf0821043049 8 21045762 5.73E-07 5.74E-07
vg1125162180 sf1124696020 11 25162180 1.16E-06 1.16E-06
vg0222522726 sf0222516857 2 22522726 1.76E-06 1.76E-06
vg1124867021 sf1124400861 11 24867021 1.94E-06 1.94E-06
vg1128277188 sf1127753967 11 28277188 2.02E-06 2.03E-06
vg1011502581 sf1011431400 10 11502581 2.04E-06 2.04E-06
vg1124774058 sf1124307898 11 24774058 2.16E-06 2.16E-06
vg1120554158 sf1120088084 11 20554158 4.76E-06 4.77E-06