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 mr1382 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
vg0804875760 sf0804874763 8 4875760 3.69E-11 1.36E-06
vg0825492911 sf0825490197 8 25492911 5.42E-11 1.42E-07
vg0506101826 sf0506101765 5 6101826 5.56E-11 NA
vg1216309552 sf1216306848 12 16309552 7.66E-11 NA
vg0310907715 sf0310906433 3 10907715 2.24E-10 NA
vg1208301005 sf1208298411 12 8301005 8.70E-09 NA
vg1216564174 sf1216561467 12 16564174 9.02E-08 3.79E-06
vg0528458618 sf0528395973 5 28458618 9.55E-08 NA
vg0703940621 sf0703939622 7 3940621 4.16E-07 4.11E-06
vg0314708663 sf0314707350 3 14708663 NA 1.13E-07
vg0328679653 sf0328672707 3 28679653 NA 3.32E-06
vg0406854032 sf0406849477 4 6854032 NA 3.54E-06
vg0109353965 sf0109352941 1 9353965 NA 4.59E-06
vg0603031631 sf0603030632 6 3031631 NA 5.97E-06