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 mr1877 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
vg0610596992 sf0610595993 6 10596992 6.30E-18 5.85E-11
vg0610566738 sf0610565739 6 10566738 2.58E-17 2.62E-11
vg0610584498 sf0610583499 6 10584498 9.98E-16 2.37E-11
vg0617303575 sf0617302578 6 17303575 7.42E-15 7.60E-07
vg0610456182 sf0610455183 6 10456182 1.33E-14 1.17E-08
vg0222739831 sf0222733962 2 22739831 1.78E-13 1.27E-16
vg0613725364 sf0613724365 6 13725364 4.23E-13 NA
vg0620412828 sf0620411831 6 20412828 4.64E-11 NA
vg0619863366 sf0619862369 6 19863366 1.34E-09 1.67E-06
vg0619861018 sf0619860021 6 19861018 1.62E-09 NA
vg0136579687 sf0136578644 1 36579687 2.46E-08 4.31E-06
vg0610606146 sf0610605147 6 10606146 9.67E-08 2.78E-06
vg0222656032 sf0222650163 2 22656032 NA 4.51E-08
vg0516027523 sf0515970031 5 16027523 NA 5.74E-07
vg0710034123 sf0710033129 7 10034123 NA 2.00E-06