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 mr1591 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
vg1014788162 sf1014716928 10 14788162 1.02E-52 3.71E-07
vg1014789603 sf1014718369 10 14789603 2.15E-52 6.86E-07
vg0332485398 sf0332478271 3 32485398 1.42E-50 NA
vg0921847884 sf0921847403 9 21847884 1.81E-50 NA
vg0827202544 sf0827199830 8 27202544 1.98E-50 NA
vg0211319190 sf0211319187 2 11319190 2.42E-50 NA
vg0626883318 sf0626882321 6 26883318 1.66E-49 NA
vg0805970126 sf0805969129 8 5970126 NA 9.01E-08
vg0528836237 sf0528773592 5 28836237 NA 1.13E-07
vg0106205427 sf0106204427 1 6205427 NA 2.93E-07
vg0400503563 sf0400502561 4 503563 NA 4.71E-07
vg1017106956 sf1017035728 10 17106956 NA 1.21E-06
vg1207875018 sf1207872424 12 7875018 NA 1.59E-06
vg0918876795 sf0918875795 9 18876795 NA 2.82E-06