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 mr1609 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
vg1124965681 sf1124499521 11 24965681 1.83E-13 3.22E-10
vg1113279889 sf1112816210 11 13279889 3.93E-08 NA
vg0819113697 sf0819110984 8 19113697 5.27E-08 NA
vg1117199869 sf1116733721 11 17199869 5.73E-08 NA
vg1110143414 sf1110137991 11 10143414 8.53E-08 NA
vg0813207586 sf0813205141 8 13207586 1.14E-07 1.24E-07
vg1109260557 sf1109255134 11 9260557 2.63E-07 NA
vg0622814690 sf0622813693 6 22814690 2.49E-06 7.91E-06
vg1207352636 sf1207350043 12 7352636 6.71E-06 2.01E-06
vg0910522913 sf0910521912 9 10522913 9.58E-06 NA