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 mr1256 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
vg0915107312 sf0915106311 9 15107312 1.33E-39 1.03E-06
vg1203947894 sf1203946893 12 3947894 4.34E-38 NA
vg0230003119 sf0229997250 2 30003119 5.06E-37 NA
vg0917623313 sf0917622312 9 17623313 9.58E-37 NA
vg0721729151 sf0721728158 7 21729151 2.13E-36 NA
vg0139928356 sf0139927313 1 39928356 1.78E-33 3.44E-06
vg0222725881 sf0222720012 2 22725881 NA 1.91E-08
vg0130736176 sf0130735132 1 30736176 NA 2.22E-07
vg0130667376 sf0130666332 1 30667376 NA 5.32E-07
vg0101295924 sf0101294924 1 1295924 NA 9.16E-07
vg0401712784 sf0401708333 4 1712784 NA 3.24E-06
vg0142338439 sf0142337395 1 42338439 NA 3.37E-06
vg0601635891 sf0601634892 6 1635891 NA 4.51E-06
vg0222628680 sf0222622811 2 22628680 NA 4.92E-06