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 mr1216 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
vg0919909230 sf0919908749 9 19909230 6.92E-21 7.27E-17
vg0919909996 sf0919909515 9 19909996 9.28E-21 2.61E-27
vg0127445565 sf0127444521 1 27445565 4.04E-15 5.75E-09
vg0721197653 sf0721196660 7 21197653 1.23E-13 6.79E-07
vg1220323426 sf1220294868 12 20323426 4.10E-10 NA
vg1021737816 sf1021666292 10 21737816 3.65E-07 2.59E-06
vg0618509087 sf0618508090 6 18509087 1.03E-06 2.45E-06
vg0628632216 sf0628631218 6 28632216 3.02E-06 1.69E-06
vg1216085140 sf1216082436 12 16085140 4.15E-06 NA
vg1100512559 sf1100511562 11 512559 7.67E-06 NA
vg0628631567 sf0628630569 6 28631567 NA 2.07E-06