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 mr1620 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
vg0719007567 sf0719006574 7 19007567 8.55E-26 2.11E-19
vg0719223576 sf0719222583 7 19223576 1.35E-13 2.30E-10
vg0719136412 sf0719135419 7 19136412 3.21E-13 5.12E-09
vg0719207675 sf0719206682 7 19207675 8.35E-12 1.53E-10
vg1201654412 sf1201653412 12 1654412 9.05E-11 5.99E-07
vg0304916753 sf0304915755 3 4916753 9.40E-11 1.32E-06
vg0304931155 sf0304930157 3 4931155 8.55E-10 1.27E-06
vg0315045169 sf0315043816 3 15045169 1.26E-09 2.03E-06
vg0719016083 sf0719015090 7 19016083 5.20E-08 9.71E-07
vg0719127230 sf0719126237 7 19127230 7.00E-08 2.24E-07
vg0719725023 sf0719724030 7 19725023 1.25E-07 1.85E-06
vg0718985954 sf0718984961 7 18985954 NA 9.00E-08
vg0719478836 sf0719477843 7 19478836 NA 1.80E-06
vg0213657300 sf0213657296 2 13657300 NA 3.96E-06
vg1109949998 sf1109944575 11 9949998 NA 7.47E-06