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 mr1639 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
vg1128511488 sf1127988267 11 28511488 1.09E-08 4.59E-06
vg0901968940 sf0901967940 9 1968940 1.56E-08 2.74E-06
vg1013317545 sf1013246314 10 13317545 7.10E-08 4.39E-06
vg0818574098 sf0818571385 8 18574098 7.34E-08 NA
vg1213045482 sf1213042821 12 13045482 8.22E-08 NA
vg0727043700 sf0727042706 7 27043700 1.29E-07 2.06E-06
vg0106725146 sf0106724146 1 6725146 1.74E-07 3.55E-06
vg0818940169 sf0818937456 8 18940169 6.22E-06 NA