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 mr1257 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
vg0216800422 sf0216794552 2 16800422 3.11E-90 1.71E-36
vg0216822884 sf0216817014 2 16822884 3.47E-90 2.88E-36
vg0719969082 sf0719968089 7 19969082 3.14E-44 NA
vg0812023942 sf0812022947 8 12023942 9.24E-44 9.25E-15
vg0900336799 sf0900335799 9 336799 4.37E-39 4.35E-10
vg1114473442 sf1114009759 11 14473442 1.87E-38 4.12E-10
vg0900337327 sf0900336327 9 337327 5.47E-38 1.29E-10
vg0216721532 sf0216715662 2 16721532 2.11E-34 1.08E-10
vg0213820023 sf0213814153 2 13820023 8.50E-32 5.33E-07
vg1219170547 sf1219142017 12 19170547 8.11E-31 NA
vg1220236581 sf1220208023 12 20236581 2.83E-30 8.86E-07
vg0217137734 sf0217131864 2 17137734 NA 4.77E-21
vg1005364262 sf1005380799 10 5364262 NA 1.02E-10
vg0216756056 sf0216750186 2 16756056 NA 5.29E-10
vg0217266536 sf0217260666 2 17266536 NA 1.95E-09
vg1105770829 sf1105766581 11 5770829 NA 1.26E-07
vg1112889066 sf1112425387 11 12889066 NA 1.79E-07
vg1213797573 sf1213794911 12 13797573 NA 4.56E-07
vg1114870126 sf1114406440 11 14870126 NA 5.11E-07
vg0217679975 sf0217674105 2 17679975 NA 6.24E-07
vg0217845805 sf0217839936 2 17845805 NA 7.25E-07
vg1010274005 sf1010202826 10 10274005 NA 8.45E-07
vg0115588570 sf0115587544 1 15588570 NA 9.64E-07
vg0714453203 sf0714452210 7 14453203 NA 1.42E-06