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 mr1074 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
vg0222741535 sf0222735666 2 22741535 2.58E-61 1.95E-22
vg0213988415 sf0213982545 2 13988415 5.76E-39 NA
vg0626585101 sf0626584104 6 26585101 1.59E-36 NA
vg0208895630 sf0208895628 2 8895630 1.99E-36 NA
vg0917346504 sf0917345503 9 17346504 1.93E-35 NA
vg0601101826 sf0601100827 6 1101826 9.20E-33 2.26E-06
vg0222628680 sf0222622811 2 22628680 NA 2.41E-10
vg0130667376 sf0130666332 1 30667376 NA 1.30E-08
vg0130832570 sf0130831526 1 30832570 NA 3.85E-08
vg0223487342 sf0223481473 2 23487342 NA 5.91E-07
vg0224868229 sf0224862360 2 24868229 NA 1.17E-06
vg0224252015 sf0224246146 2 24252015 NA 1.85E-06
vg0200800683 sf0200800683 2 800683 NA 3.82E-06
vg0222634177 sf0222628308 2 22634177 NA 4.34E-06