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 mr1317 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
vg0217155660 sf0217149790 2 17155660 8.25E-43 1.44E-25
vg0217098031 sf0217092161 2 17098031 1.38E-42 1.39E-25
vg0217116501 sf0217110631 2 17116501 2.31E-36 1.24E-21
vg0217083756 sf0217077886 2 17083756 3.56E-35 7.37E-21
vg1015182556 sf1015111324 10 15182556 3.19E-19 2.26E-07
vg1220336324 sf1220307766 12 20336324 1.06E-18 1.13E-09
vg0218833990 sf0218828121 2 18833990 1.41E-17 8.73E-06
vg0217940314 sf0217934445 2 17940314 1.23E-16 1.78E-08
vg1108225523 sf1108220133 11 8225523 3.63E-16 1.54E-07
vg0107836036 sf0107835036 1 7836036 3.75E-16 2.56E-06
vg0218642782 sf0218636913 2 18642782 1.33E-14 2.56E-07
vg1216728800 sf1216722754 12 16728800 2.53E-14 3.47E-07
vg1226816405 sf1226782804 12 26816405 2.64E-14 3.92E-06
vg1128516527 sf1127993306 11 28516527 3.07E-13 1.44E-07
vg0217233564 sf0217227694 2 17233564 2.11E-12 4.99E-06
vg0217337209 sf0217331339 2 17337209 5.12E-12 1.12E-08
vg0216808146 sf0216802276 2 16808146 1.26E-10 1.60E-07
vg0217327790 sf0217321920 2 17327790 NA 1.37E-09
vg1214800053 sf1214797394 12 14800053 NA 1.08E-06
vg0202876267 sf0202876265 2 2876267 NA 1.47E-06
vg0216239744 sf0216233874 2 16239744 NA 2.44E-06