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 mr1603 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
vg0216657284 sf0216651414 2 16657284 1.21E-13 1.95E-10
vg0216627796 sf0216621926 2 16627796 4.87E-13 7.85E-11
vg0216916686 sf0216910816 2 16916686 3.19E-11 4.64E-10
vg0121241619 sf0121240574 1 21241619 4.66E-09 NA
vg1004284387 sf1004300925 10 4284387 3.93E-08 NA
vg0209825829 sf0209825827 2 9825829 5.32E-08 NA
vg0725840534 sf0725839540 7 25840534 1.74E-07 6.75E-07
vg0322639869 sf0322638358 3 22639869 6.25E-07 1.56E-06
vg0216974254 sf0216968384 2 16974254 6.96E-07 2.82E-07
vg0106187082 sf0106186082 1 6187082 1.04E-06 1.43E-06
vg1011651673 sf1011580488 10 11651673 2.60E-06 5.39E-08
vg0216896504 sf0216890634 2 16896504 NA 1.89E-07
vg0213822498 sf0213816628 2 13822498 NA 2.28E-07
vg0317983476 sf0317982258 3 17983476 NA 2.55E-07
vg0432523372 sf0432338264 4 32523372 NA 1.12E-06
vg0518984986 sf0518922470 5 18984986 NA 1.24E-06
vg1212822297 sf1212819636 12 12822297 NA 1.97E-06