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 mr1062 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
vg0405913502 sf0405908943 4 5913502 1.07E-22 2.35E-13
vg0410659754 sf0410650454 4 10659754 4.20E-21 1.05E-11
vg1012000043 sf1011928858 10 12000043 5.66E-17 3.25E-08
vg0715481030 sf0715480037 7 15481030 6.24E-13 3.72E-06
vg0402158888 sf0402154483 4 2158888 1.83E-12 NA
vg0405539763 sf0405535204 4 5539763 5.95E-09 1.20E-09
vg0405839288 sf0405834727 4 5839288 7.59E-09 1.71E-08
vg0405180284 sf0405175726 4 5180284 7.75E-09 2.83E-06
vg0405542769 sf0405538210 4 5542769 8.96E-09 1.00E-09
vg0406361102 sf0406356542 4 6361102 6.56E-08 2.27E-07
vg0405796986 sf0405792425 4 5796986 9.67E-08 3.68E-06
vg0402474514 sf0402470113 4 2474514 5.11E-07 8.49E-07
vg0812014490 sf0812013495 8 12014490 1.20E-06 6.66E-07
vg0406995197 sf0406990468 4 6995197 1.67E-06 2.28E-06
vg0402919583 sf0402915189 4 2919583 5.09E-06 3.41E-06
vg0615397520 sf0615396521 6 15397520 NA 3.23E-06
vg0620500908 sf0620499911 6 20500908 NA 4.01E-06
vg0620733763 sf0620732766 6 20733763 NA 6.72E-06