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 mr1495 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
vg0421387824 sf0421215877 4 21387824 1.95E-14 1.38E-09
vg1008896769 sf1008825630 10 8896769 3.47E-14 4.39E-06
vg0421388196 sf0421216249 4 21388196 9.49E-14 2.79E-09
vg1006799324 sf1006814947 10 6799324 9.63E-13 4.20E-06
vg1003944398 sf1003943374 10 3944398 5.60E-12 NA
vg0504875404 sf0504875381 5 4875404 2.42E-11 4.18E-07
vg0624684756 sf0624683759 6 24684756 6.86E-10 NA
vg1002009944 sf1002008921 10 2009944 9.61E-10 1.37E-06
vg0336193973 sf0336186899 3 36193973 1.30E-09 5.75E-07
vg0219279605 sf0219273737 2 19279605 2.40E-09 1.69E-06
vg0628759426 sf0628758428 6 28759426 4.68E-09 1.75E-06
vg0133680937 sf0133679893 1 33680937 5.46E-09 9.37E-08
vg1004727190 sf1004743727 10 4727190 7.77E-09 3.41E-07
vg0906313471 sf0906312471 9 6313471 1.74E-08 6.18E-08
vg0215890449 sf0215884579 2 15890449 2.77E-08 1.44E-06
vg1120286566 sf1119820487 11 20286566 3.83E-08 1.91E-07
vg0140248597 sf0140247554 1 40248597 7.20E-08 1.34E-06
vg0303086467 sf0303085463 3 3086467 8.68E-08 3.67E-06
vg1205542061 sf1205541047 12 5542061 1.45E-07 9.21E-07
vg0219292377 sf0219286509 2 19292377 NA 6.66E-07