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 mr1709 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
vg1003173673 sf1003172650 10 3173673 5.33E-77 8.72E-50
vg1003096745 sf1003095722 10 3096745 1.10E-76 1.13E-48
vg1003521569 sf1003520546 10 3521569 2.83E-74 5.21E-51
vg0717726887 sf0717725894 7 17726887 1.54E-24 1.48E-16
vg1209942861 sf1209940271 12 9942861 1.76E-21 1.02E-12
vg0710493875 sf0710492881 7 10493875 3.24E-21 2.32E-08
vg0909393050 sf0909392049 9 9393050 1.75E-20 9.06E-10
vg0515848994 sf0515791535 5 15848994 8.88E-20 8.09E-11
vg1003115842 sf1003114819 10 3115842 2.79E-19 1.53E-14
vg1215306171 sf1215303469 12 15306171 7.89E-19 1.73E-08
vg0422509978 sf0422324865 4 22509978 4.95E-18 9.44E-10
vg1009652919 sf1009581740 10 9652919 2.00E-14 1.14E-06
vg1003189276 sf1003188253 10 3189276 8.83E-13 3.35E-07
vg1003043919 sf1003042896 10 3043919 1.84E-12 6.29E-08
vg0211784990 sf0211784986 2 11784990 3.99E-12 2.01E-07
vg1003107608 sf1003106585 10 3107608 2.44E-11 2.42E-08
vg1003509410 sf1003508387 10 3509410 3.51E-11 2.99E-07
vg0210060826 sf0210060824 2 10060826 7.33E-11 8.77E-07
vg0623387556 sf0623386559 6 23387556 2.20E-10 6.95E-09
vg1002445363 sf1002444340 10 2445363 3.24E-10 1.52E-08
vg0702358819 sf0702357820 7 2358819 2.92E-08 2.13E-06
vg1003663158 sf1003662135 10 3663158 NA 5.74E-07