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 mr1188 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
vg0222612950 sf0222607081 2 22612950 2.20E-15 1.77E-06
vg0222613010 sf0222607141 2 22613010 4.25E-15 1.24E-06
vg0113511191 sf0113510165 1 13511191 6.92E-15 NA
vg0324689010 sf0324687089 3 24689010 2.28E-13 NA
vg0124133937 sf0124132893 1 24133937 2.74E-13 4.08E-06
vg1108802682 sf1108797292 11 8802682 3.27E-13 1.01E-06
vg0235229570 sf0235223701 2 35229570 5.01E-13 2.32E-08
vg0235271495 sf0235265626 2 35271495 6.75E-13 9.42E-09
vg0124659401 sf0124658357 1 24659401 1.65E-12 1.05E-07
vg1215654794 sf1215652091 12 15654794 2.35E-12 3.82E-09
vg1108104330 sf1108100075 11 8104330 3.00E-12 8.86E-07
vg1109919219 sf1109913796 11 9919219 5.10E-11 NA
vg0320733462 sf0320731972 3 20733462 8.42E-11 4.91E-08
vg0630785612 sf0630784614 6 30785612 NA 1.30E-08
vg1108751000 sf1108745610 11 8751000 NA 2.51E-08
vg1114018010 sf1113554331 11 14018010 NA 1.63E-07
vg0235375928 sf0235370059 2 35375928 NA 2.76E-07
vg0804452573 sf0804451576 8 4452573 NA 2.98E-07
vg1020146328 sf1020074826 10 20146328 NA 6.15E-07
vg0208266410 sf0208266409 2 8266410 NA 1.48E-06
vg0235187821 sf0235181952 2 35187821 NA 1.83E-06
vg0804944075 sf0804943078 8 4944075 NA 2.15E-06
vg1006722269 sf1006737892 10 6722269 NA 2.27E-06
vg0500282325 sf0500282325 5 282325 NA 2.99E-06
vg0208253186 sf0208253185 2 8253186 NA 3.24E-06
vg1217776016 sf1217747450 12 17776016 NA 3.68E-06
vg0523699793 sf0523637214 5 23699793 NA 3.91E-06
vg0208200668 sf0208200667 2 8200668 NA 6.04E-06
vg1114456299 sf1113992616 11 14456299 NA 6.20E-06