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 mr1736 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
vg1000604182 sf1000603158 10 604182 1.01E-10 8.83E-08
vg1016114306 sf1016043078 10 16114306 1.18E-08 1.15E-07
vg1122024114 sf1121557985 11 22024114 2.79E-08 3.14E-06
vg1003625739 sf1003624716 10 3625739 9.41E-08 NA
vg0414281024 sf0414271737 4 14281024 1.02E-07 1.52E-06
vg1003719342 sf1003718319 10 3719342 1.71E-07 1.26E-06
vg1122001659 sf1121535530 11 22001659 2.73E-07 1.67E-06
vg0504952991 sf0504952969 5 4952991 9.94E-06 NA
vg0712097143 sf0712096149 7 12097143 NA 5.38E-06