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 mr1380 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
vg1117180570 sf1116714422 11 17180570 5.08E-10 2.52E-06
vg1117079321 sf1116613173 11 17079321 6.22E-10 7.83E-07
vg0122407829 sf0122406784 1 22407829 1.38E-09 NA
vg0432023544 sf0431838437 4 32023544 7.30E-09 NA
vg0122381459 sf0122380414 1 22381459 7.96E-09 NA
vg0123550945 sf0123549901 1 23550945 1.52E-08 NA
vg0122408539 sf0122407494 1 22408539 1.61E-06 NA
vg0702729357 sf0702728358 7 2729357 4.39E-06 NA
vg0410969707 sf0410960408 4 10969707 NA 7.37E-07
vg0103485561 sf0103484561 1 3485561 NA 1.87E-06
vg0916109756 sf0916108755 9 16109756 NA 2.17E-06
vg1117300240 sf1116834092 11 17300240 NA 4.72E-06