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 mr1574 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
vg0304679171 sf0304678173 3 4679171 6.24E-09 NA
vg0232480764 sf0232474895 2 32480764 2.13E-08 NA
vg0820711510 sf0820708797 8 20711510 2.30E-08 NA
vg0140469617 sf0140468574 1 40469617 2.37E-08 NA
vg0130341211 sf0130340167 1 30341211 3.10E-08 2.98E-06
vg0613864390 sf0613863391 6 13864390 3.11E-08 4.56E-06
vg0142417909 sf0142416865 1 42417909 4.55E-08 4.33E-06
vg0807801032 sf0807800036 8 7801032 2.52E-07 NA
vg1215729643 sf1215726940 12 15729643 2.53E-07 1.08E-06
vg0900523591 sf0900522591 9 523591 7.65E-07 3.25E-06
vg0128428246 sf0128427201 1 28428246 1.23E-06 1.62E-06
vg1121000159 sf1120534038 11 21000159 5.47E-06 NA
vg0608522054 sf0608521055 6 8522054 NA 2.32E-06
vg0427232971 sf0427047841 4 27232971 NA 2.63E-06