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 mr1583 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
vg0610643802 sf0610642803 6 10643802 2.74E-25 7.00E-12
vg0610429989 sf0610428990 6 10429989 2.84E-24 9.01E-13
vg0629122299 sf0629121301 6 29122299 1.56E-12 NA
vg0617359224 sf0617358227 6 17359224 2.25E-12 NA
vg0610278393 sf0610277394 6 10278393 2.85E-12 1.24E-07
vg0611796204 sf0611795205 6 11796204 1.33E-11 NA
vg0614739287 sf0614738288 6 14739287 7.03E-11 1.22E-06
vg0610590324 sf0610589325 6 10590324 1.22E-10 9.46E-07
vg0616930764 sf0616929767 6 16930764 3.25E-10 1.67E-06
vg0403221112 sf0403216715 4 3221112 3.57E-09 NA
vg0610110374 sf0610109375 6 10110374 1.27E-08 5.72E-09
vg0718838390 sf0718837397 7 18838390 1.45E-07 2.16E-06
vg0610370420 sf0610369421 6 10370420 3.08E-07 1.07E-06
vg0807272103 sf0807271108 8 7272103 8.73E-07 NA