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 mr1804 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
vg0211295378 sf0211295375 2 11295378 1.66E-10 NA
vg0127206110 sf0127205066 1 27206110 1.93E-10 2.41E-06
vg0127210847 sf0127209803 1 27210847 2.39E-10 1.53E-06
vg0127316647 sf0127315603 1 27316647 2.84E-10 4.07E-06
vg0607934967 sf0607933968 6 7934967 3.44E-10 NA
vg0420200137 sf0420028179 4 20200137 4.59E-10 NA
vg0428135712 sf0427950576 4 28135712 1.23E-09 NA
vg0431515534 sf0431330433 4 31515534 3.72E-08 2.66E-06
vg0115899007 sf0115897981 1 15899007 4.33E-08 2.73E-06
vg0104578620 sf0104577620 1 4578620 4.55E-08 NA
vg0815304114 sf0815301400 8 15304114 7.55E-08 8.93E-07
vg0432523372 sf0432338264 4 32523372 NA 4.29E-06
vg0225134433 sf0225128564 2 25134433 NA 4.32E-06
vg0432427528 sf0432242419 4 32427528 NA 5.17E-06