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 mr1211 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
vg0610752378 sf0610751379 6 10752378 1.67E-22 1.73E-19
vg0403922278 sf0403917884 4 3922278 1.50E-13 4.83E-10
vg0610469553 sf0610468554 6 10469553 1.89E-13 8.89E-09
vg0610059822 sf0610058823 6 10059822 1.65E-11 1.44E-09
vg0700906275 sf0700905275 7 906275 3.66E-10 1.18E-07
vg1006614973 sf1006630596 10 6614973 6.77E-10 NA
vg0139834469 sf0139833426 1 39834469 1.78E-09 2.24E-06
vg0617375769 sf0617374772 6 17375769 2.78E-08 4.24E-06
vg1006615974 sf1006631597 10 6615974 1.14E-07 NA
vg0718007282 sf0718006289 7 18007282 1.12E-06 3.18E-06
vg1120970935 sf1120504812 11 20970935 6.84E-06 1.32E-06
vg0717918985 sf0717917992 7 17918985 NA 3.65E-06