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 mr1924 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
vg0908998893 sf0908997892 9 8998893 7.92E-17 NA
vg0915894818 sf0915893817 9 15894818 8.01E-17 NA
vg0434838086 sf0434652977 4 34838086 1.32E-16 NA
vg0313856584 sf0313855301 3 13856584 1.46E-16 NA
vg0314592814 sf0314591501 3 14592814 1.83E-16 3.62E-06
vg0725044153 sf0725043159 7 25044153 4.02E-16 NA
vg1225855844 sf1225822239 12 25855844 2.10E-14 NA
vg0318741624 sf0318740384 3 18741624 2.29E-14 NA
vg0335809063 sf0335801932 3 35809063 2.32E-13 NA
vg0401228417 sf0401223967 4 1228417 NA 4.73E-07
vg1127497936 sf1127026323 11 27497936 NA 1.09E-06
vg0401783628 sf0401779224 4 1783628 NA 3.90E-06
vg0319372985 sf0319371496 3 19372985 NA 4.45E-06