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 mr1631 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
vg0405488386 sf0405483827 4 5488386 1.77E-10 2.34E-09
vg1219172007 sf1219143477 12 19172007 2.96E-10 1.30E-07
vg0405362835 sf0405358276 4 5362835 1.28E-09 8.75E-10
vg1218086283 sf1218057719 12 18086283 2.10E-08 NA
vg0615097742 sf0615096743 6 15097742 7.46E-08 1.30E-06
vg0703689998 sf0703688999 7 3689998 9.10E-07 1.58E-06
vg0113630238 sf0113629212 1 13630238 NA 9.23E-07