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 mr1729 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
vg1214134657 sf1214131997 12 14134657 1.37E-10 2.61E-07
vg0805546679 sf0805545682 8 5546679 1.73E-09 NA
vg0909288154 sf0909287153 9 9288154 6.86E-09 NA
vg0104048901 sf0104047901 1 4048901 7.15E-09 NA
vg0431906900 sf0431721795 4 31906900 9.36E-09 NA
vg0432427528 sf0432242419 4 32427528 1.14E-08 1.10E-06
vg0810668699 sf0810667703 8 10668699 1.35E-08 NA
vg0918880163 sf0918879163 9 18880163 3.34E-08 4.22E-06
vg0400678101 sf0400677100 4 678101 7.14E-07 3.09E-06
vg0906631032 sf0906630032 9 6631032 1.33E-06 4.19E-06
vg0518984986 sf0518922470 5 18984986 NA 4.54E-07
vg0433421279 sf0433236168 4 33421279 NA 6.73E-07
vg0400134381 sf0400133381 4 134381 NA 2.33E-06
vg1214656787 sf1214654127 12 14656787 NA 4.03E-06