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 mr1621 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
vg0724504072 sf0724503078 7 24504072 9.89E-09 4.05E-06
vg1117907473 sf1117441331 11 17907473 2.19E-08 NA
vg0916476181 sf0916475180 9 16476181 3.28E-08 NA
vg0103373486 sf0103372486 1 3373486 4.86E-08 NA
vg0801700429 sf0801699432 8 1700429 5.73E-08 NA
vg0724435404 sf0724434410 7 24435404 5.87E-08 3.87E-06
vg0906975807 sf0906974807 9 6975807 1.89E-07 4.64E-06
vg0418069623 sf0417897664 4 18069623 2.94E-06 NA