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 mr1965 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
vg1214569460 sf1214566801 12 14569460 9.74E-08 NA
vg1019855130 sf1019783630 10 19855130 2.33E-07 2.37E-06
vg0704864945 sf0704863946 7 4864945 4.10E-07 5.27E-07
vg0817557507 sf0817554793 8 17557507 1.95E-06 2.21E-06
vg0516508609 sf0516451091 5 16508609 2.16E-06 1.66E-06
vg0501973478 sf0501973460 5 1973478 2.39E-06 NA
vg0907175535 sf0907174535 9 7175535 2.90E-06 3.08E-06
vg0607659813 sf0607658814 6 7659813 3.63E-06 9.70E-07
vg0232755756 sf0232749887 2 32755756 NA 1.30E-08
vg0421020772 sf0420848825 4 21020772 NA 5.93E-07
vg0501807498 sf0501807481 5 1807498 NA 2.09E-06
vg0701288022 sf0701287022 7 1288022 NA 4.09E-06
vg0607991416 sf0607990417 6 7991416 NA 4.17E-06
vg0524795629 sf0524733044 5 24795629 NA 4.91E-06
vg0615247267 sf0615246268 6 15247267 NA 7.13E-06