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 mr1022 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
vg1215977007 sf1215974303 12 15977007 1.27E-120 3.87E-45
vg1210298965 sf1210296378 12 10298965 1.24E-60 NA
vg1209186897 sf1209184306 12 9186897 8.62E-57 8.28E-10
vg1224007541 sf1223973994 12 24007541 1.36E-52 NA
vg1212938220 sf1212935559 12 12938220 1.94E-51 NA
vg0216964004 sf0216958134 2 16964004 5.84E-45 NA
vg1223898851 sf1223865304 12 23898851 9.65E-45 2.41E-09
vg1214824840 sf1214822181 12 14824840 5.54E-40 4.54E-07
vg1215871396 sf1215868692 12 15871396 NA 1.67E-22
vg1215871822 sf1215869118 12 15871822 NA 2.94E-11
vg0610620315 sf0610619316 6 10620315 NA 2.41E-10
vg1216344388 sf1216341684 12 16344388 NA 2.33E-08
vg1216151755 sf1216149051 12 16151755 NA 6.21E-08
vg1215178345 sf1215175681 12 15178345 NA 1.55E-07
vg1214868017 sf1214865358 12 14868017 NA 2.73E-07
vg1216486981 sf1216484274 12 16486981 NA 3.12E-07
vg1215976560 sf1215973856 12 15976560 NA 3.31E-07
vg1216545585 sf1216542878 12 16545585 NA 3.80E-07
vg1216037905 sf1216035201 12 16037905 NA 1.14E-06
vg1216409400 sf1216406693 12 16409400 NA 1.16E-06
vg0123696065 sf0123695021 1 23696065 NA 1.24E-06
vg1217221999 sf1217215954 12 17221999 NA 1.27E-06
vg0403224975 sf0403220578 4 3224975 NA 1.27E-06
vg1217374273 sf1217368228 12 17374273 NA 1.64E-06
vg1215515938 sf1215513235 12 15515938 NA 1.89E-06
vg1217281529 sf1217275484 12 17281529 NA 2.46E-06
vg1214986204 sf1214983546 12 14986204 NA 2.65E-06