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 mr1669 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
vg0232208358 sf0232202489 2 32208358 2.06E-08 5.29E-06
vg0421294092 sf0421122146 4 21294092 3.28E-08 NA
vg0421454162 sf0421282213 4 21454162 6.34E-08 NA
vg0403204105 sf0403199708 4 3204105 3.95E-07 7.83E-06
vg0421291900 sf0421119954 4 21291900 4.34E-07 4.19E-06
vg0516563624 sf0516506106 5 16563624 1.14E-06 1.62E-06
vg0516302066 sf0516244548 5 16302066 1.35E-06 NA
vg0141969878 sf0141968835 1 41969878 4.36E-06 3.48E-07
vg0203358788 sf0203358786 2 3358788 6.10E-06 1.70E-06
vg0712843936 sf0712842943 7 12843936 7.47E-06 3.36E-06
vg0431043984 sf0430858869 4 31043984 NA 9.66E-07