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 mr1446 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
vg1116564255 sf1116099133 11 16564255 1.51E-13 NA
vg0202909303 sf0202909301 2 2909303 6.53E-13 NA
vg0522983676 sf0522921117 5 22983676 7.47E-13 NA
vg0520082492 sf0520019968 5 20082492 1.73E-12 NA
vg0608277816 sf0608276817 6 8277816 2.19E-12 NA
vg1012297597 sf1012226412 10 12297597 4.57E-11 3.33E-06
vg1012239875 sf1012168690 10 12239875 1.30E-10 1.24E-06
vg0608278039 sf0608277040 6 8278039 1.32E-10 NA
vg0224478551 sf0224472682 2 24478551 1.23E-08 1.18E-06
vg1010068253 sf1009997074 10 10068253 6.61E-08 NA
vg0820146322 sf0820143609 8 20146322 NA 1.21E-07
vg1121036873 sf1120570752 11 21036873 NA 3.72E-06
vg0103143509 sf0103142509 1 3143509 NA 4.97E-06