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 mr1587 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
vg0314559038 sf0314557726 3 14559038 2.93E-36 7.54E-20
vg0314576905 sf0314575592 3 14576905 4.45E-35 1.37E-20
vg0104719031 sf0104718031 1 4719031 2.42E-25 1.86E-06
vg0422485909 sf0422300796 4 22485909 5.35E-24 NA
vg0605259601 sf0605258602 6 5259601 2.57E-23 1.81E-06
vg0825285146 sf0825282432 8 25285146 3.42E-23 NA
vg0605314203 sf0605313204 6 5314203 5.09E-23 1.70E-07
vg0129972238 sf0129971193 1 29972238 7.74E-23 6.28E-07
vg0104989336 sf0104988336 1 4989336 8.37E-22 2.40E-08
vg0825118700 sf0825115986 8 25118700 2.21E-20 NA
vg0314576860 sf0314575547 3 14576860 4.88E-19 7.49E-09
vg1215558096 sf1215555393 12 15558096 9.29E-18 NA
vg0208903558 sf0208903556 2 8903558 1.20E-15 NA
vg0314498825 sf0314497513 3 14498825 NA 4.36E-11
vg0314382891 sf0314381580 3 14382891 NA 5.42E-08
vg0104996735 sf0104995735 1 4996735 NA 7.50E-08
vg0314415225 sf0314413914 3 14415225 NA 3.24E-07
vg0314488405 sf0314487093 3 14488405 NA 1.50E-06
vg0714418395 sf0714417402 7 14418395 NA 1.57E-06
vg0910358590 sf0910357589 9 10358590 NA 2.57E-06
vg0523655696 sf0523593117 5 23655696 NA 2.86E-06