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 mr1758 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
vg1113239034 sf1112775355 11 13239034 1.89E-09 3.61E-07
vg1111074881 sf1111069198 11 11074881 6.71E-09 1.77E-07
vg0801098187 sf0801097189 8 1098187 1.36E-08 5.76E-08
vg0801276119 sf0801275121 8 1276119 1.47E-08 5.24E-06
vg1105601806 sf1105597558 11 5601806 2.34E-08 NA
vg0821985309 sf0821982596 8 21985309 1.09E-07 1.20E-06
vg0214609392 sf0214603522 2 14609392 4.54E-07 8.11E-08
vg0714437365 sf0714436372 7 14437365 6.74E-07 9.51E-07
vg1111023509 sf1111017826 11 11023509 9.48E-07 2.76E-06
vg1015010798 sf1014939564 10 15010798 9.79E-07 3.44E-06
vg0432816051 sf0432630937 4 32816051 1.73E-06 1.15E-06
vg0524661216 sf0524598636 5 24661216 2.02E-06 9.20E-07
vg0406068144 sf0406063583 4 6068144 3.45E-06 2.49E-06
vg0906731412 sf0906730412 9 6731412 6.39E-06 NA
vg1215106968 sf1215104305 12 15106968 7.32E-06 2.71E-06
vg1100988118 sf1100987119 11 988118 NA 9.03E-07
vg1005048726 sf1005065263 10 5048726 NA 1.90E-06
vg0631247242 sf0631246244 6 31247242 NA 1.96E-06
vg1221303134 sf1221269681 12 21303134 NA 2.82E-06