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 mr1068 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 1.01E-23 3.06E-20
vg0610460953 sf0610459954 6 10460953 2.27E-11 8.70E-09
vg0403922278 sf0403917884 4 3922278 3.24E-11 1.38E-08
vg0610059822 sf0610058823 6 10059822 8.46E-11 3.50E-10
vg0626895745 sf0626894748 6 26895745 3.06E-10 1.29E-09
vg1006614973 sf1006630596 10 6614973 6.49E-09 2.26E-06
vg0700906275 sf0700905275 7 906275 7.89E-09 1.12E-07
vg1222906823 sf1222873262 12 22906823 8.20E-09 9.07E-07
vg0223178015 sf0223172146 2 23178015 1.48E-08 1.77E-06
vg0126649568 sf0126648524 1 26649568 3.15E-08 2.97E-06
vg1202381362 sf1202380363 12 2381362 5.02E-08 1.71E-06
vg0308121921 sf0308120859 3 8121921 1.11E-07 2.22E-06
vg0523732368 sf0523669789 5 23732368 1.27E-07 4.61E-06
vg0629851797 sf0629850799 6 29851797 1.40E-07 2.62E-07
vg0617909927 sf0617908930 6 17909927 1.54E-07 2.17E-06
vg1205756282 sf1205755264 12 5756282 2.14E-07 1.60E-06
vg0208618283 sf0208618282 2 8618283 3.79E-07 4.02E-06
vg0707975245 sf0707974250 7 7975245 4.70E-07 1.41E-07
vg0910025779 sf0910024778 9 10025779 1.92E-06 3.19E-06
vg0228232599 sf0228226730 2 28232599 3.03E-06 3.37E-06