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 mr1874 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
vg0825135910 sf0825133196 8 25135910 2.32E-81 1.92E-34
vg0825038970 sf0825036256 8 25038970 3.07E-81 1.37E-35
vg0217789129 sf0217783260 2 17789129 3.76E-28 NA
vg0103847902 sf0103846902 1 3847902 3.07E-27 NA
vg0804053856 sf0804052859 8 4053856 6.58E-26 NA
vg1009610847 sf1009539668 10 9610847 1.32E-25 9.92E-07
vg0705701933 sf0705700934 7 5701933 2.64E-25 1.60E-07
vg0825230903 sf0825228189 8 25230903 3.15E-22 3.78E-07
vg0824984265 sf0824981551 8 24984265 1.36E-18 6.02E-13
vg0825087446 sf0825084732 8 25087446 NA 1.25E-22
vg0825541162 sf0825538448 8 25541162 NA 8.93E-10
vg0905354568 sf0905353568 9 5354568 NA 4.02E-08
vg0905075837 sf0905074837 9 5075837 NA 1.23E-07
vg0320043666 sf0320042177 3 20043666 NA 6.14E-07
vg0316396424 sf0316395069 3 16396424 NA 1.10E-06
vg0412624645 sf0412615355 4 12624645 NA 1.74E-06
vg0826228310 sf0826225596 8 26228310 NA 2.23E-06
vg0826039982 sf0826037268 8 26039982 NA 2.65E-06
vg0432523372 sf0432338264 4 32523372 NA 3.05E-06
vg0825022011 sf0825019297 8 25022011 NA 3.54E-06
vg0115899007 sf0115897981 1 15899007 NA 4.09E-06
vg0334068822 sf0334061692 3 34068822 NA 4.12E-06
vg0825213870 sf0825211156 8 25213870 NA 4.35E-06