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 mr1661 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
vg0821970212 sf0821967499 8 21970212 1.75E-08 4.82E-06
vg0218624032 sf0218618163 2 18624032 2.61E-08 NA
vg1105129212 sf1105125023 11 5129212 4.71E-07 2.08E-06
vg0526989740 sf0526927096 5 26989740 3.90E-06 6.52E-07
vg0911168190 sf0911167189 9 11168190 8.07E-06 3.22E-06
vg0814295706 sf0814292992 8 14295706 NA 4.99E-06