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 mr1280 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
vg0131785830 sf0131784786 1 31785830 1.28E-09 2.15E-07
vg1121038115 sf1120571994 11 21038115 5.16E-09 NA
vg1205136836 sf1205135822 12 5136836 6.17E-08 3.92E-07
vg1214823803 sf1214821144 12 14823803 6.59E-08 NA
vg0826160404 sf0826157690 8 26160404 1.53E-07 1.48E-07
vg0110800593 sf0110799569 1 10800593 3.87E-07 2.21E-06
vg0140126851 sf0140125808 1 40126851 1.00E-06 1.16E-06
vg0615411425 sf0615410426 6 15411425 2.51E-06 2.75E-07
vg0315253958 sf0315252605 3 15253958 NA 6.04E-07