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 mr1819 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
vg0917838619 sf0917837618 9 17838619 2.46E-16 NA
vg0429558768 sf0429373636 4 29558768 4.34E-15 NA
vg0424075113 sf0423889974 4 24075113 5.00E-15 NA
vg0123462204 sf0123461160 1 23462204 1.21E-14 NA
vg1126048564 sf1125576978 11 26048564 2.21E-14 NA
vg0406065801 sf0406061240 4 6065801 2.43E-12 6.51E-06
vg1218208697 sf1218180133 12 18208697 NA 1.44E-07
vg1013579563 sf1013508333 10 13579563 NA 2.24E-07
vg1218191046 sf1218162482 12 18191046 NA 8.19E-07
vg1209434696 sf1209432105 12 9434696 NA 1.24E-06
vg1209892674 sf1209890084 12 9892674 NA 1.59E-06
vg0817998222 sf0817995509 8 17998222 NA 3.21E-06
vg0312105071 sf0312103789 3 12105071 NA 4.12E-06
vg0312113974 sf0312112692 3 12113974 NA 5.65E-06