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 mr1735 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
vg0318146978 sf0318145760 3 18146978 4.33E-12 6.65E-06
vg1106493327 sf1106489079 11 6493327 5.72E-10 NA
vg0506417689 sf0506417629 5 6417689 9.27E-10 NA
vg0400814559 sf0400813559 4 814559 2.24E-09 NA
vg1019739673 sf1019668173 10 19739673 2.94E-09 NA
vg0319293489 sf0319292249 3 19293489 3.56E-07 NA
vg0423651585 sf0423466442 4 23651585 7.15E-07 8.57E-07
vg0800635903 sf0800634903 8 635903 NA 1.07E-06
vg0719198353 sf0719197360 7 19198353 NA 3.33E-06
vg0719140779 sf0719139786 7 19140779 NA 4.08E-06
vg1022845266 sf1022773739 10 22845266 NA 5.02E-06
vg0204458881 sf0204458878 2 4458881 NA 5.17E-06
vg1011728450 sf1011657265 10 11728450 NA 7.37E-06