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 mr1301 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
vg0417238354 sf0417066395 4 17238354 2.48E-57 3.02E-28
vg0519939017 sf0519876493 5 19939017 6.27E-38 8.48E-20
vg0608700390 sf0608699391 6 8700390 9.78E-37 3.46E-14
vg0722183786 sf0722182793 7 22183786 1.89E-36 4.08E-15
vg0401797174 sf0401792769 4 1797174 6.28E-36 8.39E-15
vg0406753488 sf0406748934 4 6753488 2.13E-34 1.45E-15
vg0718478602 sf0718477609 7 18478602 6.42E-34 1.59E-12
vg0410354028 sf0410344727 4 10354028 1.25E-33 5.17E-16
vg0211588654 sf0211588650 2 11588654 4.71E-33 1.95E-15
vg0707065048 sf0707064053 7 7065048 2.35E-32 1.17E-09
vg0309190281 sf0309189217 3 9190281 8.98E-31 4.25E-10
vg0905616909 sf0905615909 9 5616909 3.00E-29 2.74E-10
vg0801480069 sf0801479071 8 1480069 4.44E-27 9.53E-10
vg0507786958 sf0507786899 5 7786958 1.41E-26 8.12E-11
vg0506581374 sf0506581315 5 6581374 8.18E-25 1.27E-06
vg1013723877 sf1013652646 10 13723877 8.53E-25 3.65E-10
vg0817661668 sf0817658955 8 17661668 8.90E-25 1.35E-09
vg0518975375 sf0518912859 5 18975375 NA 3.31E-11
vg0417132051 sf0416960092 4 17132051 NA 3.60E-10
vg0212006137 sf0212006133 2 12006137 NA 1.43E-09
vg0419225907 sf0419053945 4 19225907 NA 2.60E-09
vg0728385374 sf0728384382 7 28385374 NA 2.23E-08
vg0502285064 sf0502285039 5 2285064 NA 6.91E-07