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 mr1496 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
vg1008794614 sf1008723476 10 8794614 3.24E-14 1.04E-07
vg0110929029 sf0110928005 1 10929029 5.63E-11 NA
vg0813652329 sf0813649614 8 13652329 7.65E-11 NA
vg0610960628 sf0610959629 6 10960628 1.46E-10 1.98E-06
vg0142683989 sf0142682945 1 42683989 2.46E-10 NA
vg1202108506 sf1202107504 12 2108506 8.59E-10 1.06E-06
vg0220933168 sf0220927300 2 20933168 3.49E-08 6.57E-07
vg0415195707 sf0414570345 4 15195707 6.51E-08 NA
vg1202199834 sf1202198833 12 2199834 8.83E-08 1.19E-06
vg1216729892 sf1216723846 12 16729892 9.12E-07 6.99E-07
vg0610442617 sf0610441618 6 10442617 NA 3.56E-06
vg0223559507 sf0223553638 2 23559507 NA 4.19E-06