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 mr1733 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
vg0705537793 sf0705536794 7 5537793 1.37E-70 NA
vg0211287530 sf0211287527 2 11287530 1.08E-69 NA
vg0304934966 sf0304933968 3 4934966 3.61E-69 NA
vg0107138425 sf0107137425 1 7138425 7.63E-69 NA
vg0307947851 sf0307946789 3 7947851 1.09E-67 NA
vg0304934277 sf0304933279 3 4934277 7.08E-67 NA
vg0502606736 sf0502606712 5 2606736 3.02E-64 3.97E-08
vg0132368333 sf0132367289 1 32368333 4.48E-64 3.19E-06
vg1017941557 sf1017870329 10 17941557 3.78E-63 NA
vg0216773157 sf0216767287 2 16773157 9.66E-62 5.11E-07
vg0917087568 sf0917086567 9 17087568 NA 1.27E-10
vg0107249555 sf0107248555 1 7249555 NA 7.76E-08
vg0219806820 sf0219800952 2 19806820 NA 2.94E-07
vg0124680654 sf0124679610 1 24680654 NA 3.34E-07
vg0624687214 sf0624686217 6 24687214 NA 3.43E-07
vg0326757569 sf0326750623 3 26757569 NA 4.28E-07
vg1125281578 sf1124815418 11 25281578 NA 4.52E-07
vg0709586016 sf0709585022 7 9586016 NA 5.82E-07
vg0228498409 sf0228492540 2 28498409 NA 7.00E-07
vg0815549377 sf0815546663 8 15549377 NA 8.33E-07
vg1219133094 sf1219104530 12 19133094 NA 1.10E-06
vg0917493665 sf0917492664 9 17493665 NA 1.16E-06
vg0107057516 sf0107056516 1 7057516 NA 1.18E-06
vg1008018769 sf1008025468 10 8018769 NA 1.19E-06
vg0414604268 sf0414594982 4 14604268 NA 1.23E-06
vg0718620468 sf0718619475 7 18620468 NA 1.40E-06
vg0216156343 sf0216150473 2 16156343 NA 1.52E-06
vg0919040682 sf0919040271 9 19040682 NA 1.56E-06
vg0611856752 sf0611855753 6 11856752 NA 1.73E-06
vg1214781092 sf1214778433 12 14781092 NA 1.74E-06
vg1108531956 sf1108526566 11 8531956 NA 2.62E-06
vg0709968476 sf0709967482 7 9968476 NA 3.23E-06
vg0124729720 sf0124728676 1 24729720 NA 5.35E-06