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 mr1031 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
vg0130113615 sf0130112570 1 30113615 2.63E-11 NA
vg1218287520 sf1218258956 12 18287520 9.60E-10 NA
vg0138103681 sf0138102638 1 38103681 1.50E-09 NA
vg1222399044 sf1222365483 12 22399044 1.81E-09 NA
vg0217651623 sf0217645753 2 17651623 2.86E-09 NA
vg0138093125 sf0138092082 1 38093125 4.06E-08 1.87E-06
vg1218169210 sf1218140646 12 18169210 2.42E-07 NA
vg0701530964 sf0701529964 7 1530964 1.32E-06 NA
vg1208270538 sf1208267943 12 8270538 1.35E-06 NA
vg1121673447 sf1121207324 11 21673447 2.21E-06 NA