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 mr1949 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
vg0719065500 sf0719064507 7 19065500 4.71E-15 1.79E-16
vg0719006525 sf0719005532 7 19006525 2.99E-14 8.31E-13
vg0719040385 sf0719039392 7 19040385 3.63E-14 1.57E-16
vg0719041786 sf0719040793 7 19041786 2.72E-13 1.55E-11
vg0107198487 sf0107197487 1 7198487 8.42E-09 NA
vg1101991503 sf1101987361 11 1991503 4.03E-08 7.77E-07
vg1101911438 sf1101910439 11 1911438 6.27E-08 1.60E-07
vg0328527072 sf0328520125 3 28527072 7.80E-08 NA
vg0125159819 sf0125158775 1 25159819 NA 8.48E-07
vg0329561125 sf0329554165 3 29561125 NA 2.20E-06
vg0900544466 sf0900543466 9 544466 NA 3.15E-06
vg0123496391 sf0123495347 1 23496391 NA 3.29E-06
vg0422276479 sf0422091361 4 22276479 NA 3.70E-06
vg1214800170 sf1214797511 12 14800170 NA 4.13E-06