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 mr1177 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
vg1210798384 sf1210795750 12 10798384 1.35E-09 NA
vg1204484263 sf1204483251 12 4484263 3.78E-09 NA
vg1213545780 sf1213543118 12 13545780 4.14E-09 NA
vg0706198216 sf0706197217 7 6198216 4.37E-09 NA
vg1210885192 sf1210882558 12 10885192 4.72E-09 NA
vg0607428368 sf0607427369 6 7428368 3.44E-08 4.15E-06
vg0335059768 sf0335052638 3 35059768 2.09E-07 7.45E-06
vg0822310706 sf0822307993 8 22310706 2.61E-07 9.24E-06
vg1000986102 sf1000985078 10 986102 1.23E-06 2.10E-06
vg0728897313 sf0728896321 7 28897313 3.72E-06 NA
vg0413193060 sf0413183770 4 13193060 4.33E-06 4.31E-06
vg1122497642 sf1122031513 11 22497642 NA 1.52E-06
vg0805761726 sf0805760729 8 5761726 NA 2.60E-06