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 mr1566 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
vg0715681504 sf0715680511 7 15681504 2.16E-21 NA
vg0612956044 sf0612955045 6 12956044 3.21E-21 NA
vg0812798675 sf0812796500 8 12798675 4.65E-21 3.41E-07
vg0305033997 sf0305032999 3 5033997 1.75E-20 NA
vg0802224907 sf0802223910 8 2224907 2.25E-20 NA
vg1124875808 sf1124409648 11 24875808 2.02E-17 1.16E-07
vg1125118463 sf1124652303 11 25118463 NA 1.06E-07
vg0812798828 sf0812796653 8 12798828 NA 3.14E-07
vg0623662680 sf0623661683 6 23662680 NA 6.75E-07
vg0623662684 sf0623661687 6 23662684 NA 8.29E-07
vg1124986792 sf1124520632 11 24986792 NA 2.03E-06
vg0810603358 sf0810602362 8 10603358 NA 2.25E-06
vg1125113390 sf1124647230 11 25113390 NA 2.42E-06
vg0101045975 sf0101044975 1 1045975 NA 2.54E-06
vg1125031400 sf1124565240 11 25031400 NA 2.93E-06
vg1125838229 sf1125372148 11 25838229 NA 4.29E-06
vg1124988728 sf1124522568 11 24988728 NA 4.57E-06
vg0106309143 sf0106308143 1 6309143 NA 8.48E-06