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 mr1672 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
vg0138439876 sf0138438833 1 38439876 6.04E-11 1.76E-07
vg0421386227 sf0421214280 4 21386227 3.63E-10 1.46E-07
vg0810521627 sf0810520631 8 10521627 3.90E-10 1.36E-07
vg0815688233 sf0815685519 8 15688233 5.20E-10 2.54E-07
vg1226008690 sf1225975084 12 26008690 1.65E-09 1.05E-07
vg1116469864 sf1116004741 11 16469864 5.81E-09 3.94E-06
vg0819590125 sf0819587412 8 19590125 8.04E-09 3.56E-06
vg1123889289 sf1123423159 11 23889289 1.55E-08 1.81E-06
vg0138415477 sf0138414434 1 38415477 6.74E-08 5.29E-07
vg0710389112 sf0710388118 7 10389112 1.81E-07 7.56E-07
vg0307547080 sf0307546018 3 7547080 NA 4.07E-06