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 mr1012 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
vg0908237885 sf0908236885 9 8237885 6.71E-08 5.35E-08
vg0309106481 sf0309105417 3 9106481 1.52E-07 2.40E-06
vg0212300877 sf0212300873 2 12300877 2.11E-07 7.30E-08
vg1204159224 sf1204158212 12 4159224 6.12E-07 8.07E-07
vg0314683652 sf0314682339 3 14683652 7.32E-07 2.34E-06
vg0515261196 sf0515203738 5 15261196 1.05E-06 1.04E-06
vg1111823191 sf1111817508 11 11823191 1.85E-06 7.49E-07
vg0220043147 sf0220037279 2 20043147 2.55E-06 2.26E-07
vg0421045057 sf0420873111 4 21045057 2.90E-06 8.81E-07
vg0623214938 sf0623213941 6 23214938 2.96E-06 2.12E-06
vg0501245720 sf0501245704 5 1245720 3.07E-06 3.22E-06
vg1111465097 sf1111459414 11 11465097 3.15E-06 2.43E-06
vg0209208522 sf0209208520 2 9208522 4.62E-06 2.27E-07
vg0822468473 sf0822465760 8 22468473 4.73E-06 4.04E-06
vg1111511705 sf1111506022 11 11511705 5.48E-06 4.35E-06
vg0806624976 sf0806623981 8 6624976 7.87E-06 1.41E-06
vg1003042576 sf1003041553 10 3042576 8.11E-06 5.79E-07
vg1001623967 sf1001622944 10 1623967 8.40E-06 4.58E-07
vg1208985713 sf1208983121 12 8985713 9.07E-06 4.08E-06
vg0716104225 sf0716103232 7 16104225 NA 4.53E-06
vg0207460210 sf0207460210 2 7460210 NA 6.42E-06