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 mr1855 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
vg0217093461 sf0217087591 2 17093461 1.49E-146 2.21E-58
vg0217102196 sf0217096326 2 17102196 2.51E-140 4.07E-62
vg1015182556 sf1015111324 10 15182556 3.25E-57 6.82E-09
vg1220336324 sf1220307766 12 20336324 9.48E-55 3.06E-10
vg1226816492 sf1226782891 12 26816492 7.06E-47 2.98E-08
vg0107836036 sf0107835036 1 7836036 6.36E-41 2.50E-07
vg1103133067 sf1103128970 11 3133067 1.40E-31 1.98E-07
vg1216728800 sf1216722754 12 16728800 4.84E-31 1.04E-09
vg0217344818 sf0217338948 2 17344818 4.40E-25 1.51E-15
vg1005364284 sf1005380821 10 5364284 6.44E-25 1.23E-07
vg0216163461 sf0216157591 2 16163461 7.50E-25 2.08E-11
vg0216754099 sf0216748229 2 16754099 2.38E-23 4.27E-08
vg0217937456 sf0217931587 2 17937456 5.09E-23 3.53E-12
vg0217144860 sf0217138990 2 17144860 1.09E-22 2.00E-33
vg0217474288 sf0217468418 2 17474288 1.86E-19 1.40E-09
vg0213253468 sf0213253464 2 13253468 3.68E-19 6.01E-10
vg0512377294 sf0512377224 5 12377294 8.43E-19 3.47E-07
vg0215779498 sf0215773628 2 15779498 1.48E-18 2.26E-08
vg0217345118 sf0217339248 2 17345118 NA 1.58E-11
vg0217919982 sf0217914113 2 17919982 NA 1.02E-08
vg0417133455 sf0416961496 4 17133455 NA 4.02E-07
vg0432620685 sf0432435575 4 32620685 NA 6.21E-06