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 mr1873 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
vg0506882545 sf0506882487 5 6882545 2.55E-12 1.88E-07
vg0506882220 sf0506882162 5 6882220 4.74E-12 5.56E-08
vg0427936017 sf0427750880 4 27936017 3.08E-09 1.68E-06
vg0500459100 sf0500459100 5 459100 4.35E-09 4.78E-06
vg0427886354 sf0427701216 4 27886354 1.08E-08 1.04E-07
vg0327721881 sf0327714934 3 27721881 2.87E-08 NA
vg0916310811 sf0916309810 9 16310811 5.85E-08 1.14E-06
vg0408380930 sf0408376204 4 8380930 2.21E-06 1.99E-06
vg0130239724 sf0130238679 1 30239724 6.34E-06 5.24E-07
vg0331267762 sf0331260647 3 31267762 7.06E-06 2.23E-06
vg1116521139 sf1116056016 11 16521139 NA 2.32E-07
vg0428451299 sf0428266152 4 28451299 NA 1.41E-06
vg0100300455 sf0100299455 1 300455 NA 4.74E-06