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 mr1178 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 1.67E-222 5.05E-75
vg1210219854 sf1210217266 12 10219854 5.38E-113 1.63E-07
vg1210345550 sf1210342963 12 10345550 1.35E-112 1.82E-09
vg0217092666 sf0217086796 2 17092666 7.54E-95 NA
vg1224007541 sf1223973994 12 24007541 1.90E-91 NA
vg1018567403 sf1018495960 10 18567403 2.22E-80 NA
vg1215857575 sf1215854871 12 15857575 NA 6.07E-32
vg1215969757 sf1215967053 12 15969757 NA 4.40E-17
vg1215871822 sf1215869118 12 15871822 NA 2.22E-13
vg1216344388 sf1216341684 12 16344388 NA 3.70E-12
vg0610620315 sf0610619316 6 10620315 NA 1.09E-11
vg1216346285 sf1216343581 12 16346285 NA 1.07E-10
vg1216151755 sf1216149051 12 16151755 NA 8.78E-10
vg1216257098 sf1216254394 12 16257098 NA 2.90E-09
vg0920348485 sf0920348004 9 20348485 NA 5.07E-09
vg1215135668 sf1215133004 12 15135668 NA 2.19E-08
vg1216409400 sf1216406693 12 16409400 NA 3.22E-08
vg1216176025 sf1216173321 12 16176025 NA 3.70E-08
vg1216596256 sf1216593549 12 16596256 NA 7.51E-08
vg1212876949 sf1212874288 12 12876949 NA 8.59E-08
vg1216413575 sf1216410868 12 16413575 NA 1.15E-07
vg1217063939 sf1217057894 12 17063939 NA 1.44E-07
vg1216530604 sf1216527897 12 16530604 NA 1.66E-07
vg1215763538 sf1215760835 12 15763538 NA 1.77E-07
vg1212873614 sf1212870953 12 12873614 NA 2.05E-07
vg1216273753 sf1216271049 12 16273753 NA 4.27E-07