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 mr1011 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
vg0602961865 sf0602960866 6 2961865 5.77E-08 NA
vg0131981015 sf0131979971 1 31981015 7.24E-08 NA
vg0908237885 sf0908236885 9 8237885 7.74E-08 1.07E-07
vg0212300877 sf0212300873 2 12300877 9.39E-08 5.19E-09
vg0728961469 sf0728960477 7 28961469 1.97E-07 NA
vg1111465097 sf1111459414 11 11465097 4.09E-07 3.81E-07
vg1204159224 sf1204158212 12 4159224 1.08E-06 2.18E-06
vg0314683652 sf0314682339 3 14683652 1.16E-06 5.85E-06
vg0822468473 sf0822465760 8 22468473 1.79E-06 8.86E-07
vg0220043147 sf0220037279 2 20043147 2.01E-06 8.72E-09
vg0501245720 sf0501245704 5 1245720 4.20E-06 2.07E-06
vg1111511705 sf1111506022 11 11511705 8.15E-06 2.67E-06
vg1121560983 sf1121094860 11 21560983 9.38E-06 1.53E-06
vg0209208522 sf0209208520 2 9208522 9.96E-06 3.39E-07
vg0706877418 sf0706876423 7 6877418 NA 1.24E-07
vg1003042576 sf1003041553 10 3042576 NA 3.69E-07
vg0823149834 sf0823147121 8 23149834 NA 4.93E-07
vg1001623967 sf1001622944 10 1623967 NA 5.06E-07
vg0109422374 sf0109421350 1 9422374 NA 8.33E-07
vg0513951648 sf0513894192 5 13951648 NA 9.00E-07
vg0600002758 sf0600001758 6 2758 NA 1.16E-06
vg0234219499 sf0234213630 2 34219499 NA 2.01E-06
vg0713636558 sf0713635565 7 13636558 NA 2.78E-06
vg1213201641 sf1213198979 12 13201641 NA 2.91E-06
vg0716104225 sf0716103232 7 16104225 NA 3.25E-06
vg0233398824 sf0233392955 2 33398824 NA 5.01E-06